NCBI Homo sapiens Annotation Release GCF_000001405.40-RS_2023_10
The genome sequence records for Homo sapiens RefSeq assembly GCF_000001405.40 (GRCh38.p14) were annotated by the NCBI Eukaryotic Genome Annotation
Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies.
Annotation Release GCF_000001405.40-RS_2023_10 is an update of NCBI Homo sapiens Annotation Release 110. The known RefSeq transcripts (with NM_ and NR_ prefixes) that were current on Oct 2 2023 were placed on the genome and used to update the annotated features. In addition, model RefSeq predicted in the last full annotation (NCBI Homo sapiens Annotation Release 110) that were still current on Oct 2 2023 were included in the updated annotation. These models were not re-calculated for this update. For more information on the evidence used for generating the model RefSeq, please consult the report for NCBI Homo sapiens Annotation Release 110.
The annotation products are available in the sequence databases and on the
FTP site.
This report provides:
For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline
page.
Annotation Release information
This annotation should be referred to as "GCF_000001405.40-RS_2023_10".
Date of Entrez queries for transcripts and proteins: Oct 2 2023
Date of submission of annotation to the public databases: Oct 6 2023
Software version: 10.2
Assemblies
The following assemblies were included in this annotation run:
| Assembly name | Assembly accession | Submitter | Assembly date | Reference/Alternate | Assembly content |
|---|
| GRCh38.p14 | GCF_000001405.40 | Genome Reference Consortium | 02-03-2022 | Reference | 25 assembled chromosomes; unplaced scaffolds |
| T2T-CHM13v2.0 | GCF_009914755.1 | T2T Consortium | 01-24-2022 | Alternate | 24 assembled chromosomes |
Gene and feature statistics
Counts and length of annotated features are provided below for each assembly.
Feature counts
| Feature | GRCh38.p14 | GRCh38.p14
Primary Assembly | GRCh38.p14
All Alt Loci | GRCh38.p14
PATCHES | T2T-CHM13v2.0 |
|---|
Genes and pseudogenes  | 59,652 | 59,031 | 2,518 | 2,878 | 58,360 |
| protein-coding | 20,080 | 19,895 | 861 | 1,089 | 20,077 |
| non-coding | 22,102 | 21,795 | 730 | 867 | 20,939 |
| Transcribed pseudogenes | 1,225 | 1,224 | 103 | 151 | 1,204 |
| Non-transcribed pseudogenes | 15,772 | 15,655 | 654 | 736 | 15,683 |
| genes with variants | 20,229 | 20,027 | 725 | 850 | 20,245 |
| Immunoglobulin/T-cell receptor gene segments | 400 | 390 | 162 | 24 | 387 |
| other | 73 | 72 | 8 | 11 | 70 |
| placed on multiple assembly-units | 4,458 | na | 674 | na | na |
| mRNAs | 136,181 | 130,442 | 5,634 | 4,637 | 129,663 |
| fully-supported | 132,914 | 127,691 | 5,352 | 4,403 | 124,799 |
| with > 5% ab initio | 1,248 | 1,074 | 92 | 82 | 1,121 |
| partial | 31 | 71 | 312 | 315 | 121 |
| with filled gap(s) | 0 | 0 | 0 | 0 | 0 |
| placed on multiple assembly-units | 4,296 | na | 810 | na | na |
| known RefSeq (NM_) | 67,116 | 66,976 | 2,110 | 2,562 | 66,971 |
| model RefSeq (XM_) | 69,065 | 63,466 | 3,524 | 2,075 | 62,692 |
| non-coding RNAs | 49,182 | 46,564 | 1,958 | 1,780 | 48,943 |
| fully-supported | 46,068 | 44,182 | 1,574 | 1,613 | 45,616 |
| with > 5% ab initio | 0 | 0 | 0 | 0 | 0 |
| partial | 9 | 9 | 82 | 64 | 43 |
| with filled gap(s) | 0 | 0 | 0 | 0 | 0 |
| placed on multiple assembly-units | 1,085 | na | 222 | na | na |
| known RefSeq (NR_) | 21,487 | 21,477 | 642 | 669 | 21,434 |
| model RefSeq (XR_) | 25,697 | 23,694 | 981 | 1,022 | 26,027 |
| pseudo transcripts | 1,756 | 1,720 | 130 | 188 | 1,685 |
| fully-supported | 1,735 | 1,704 | 127 | 186 | 1,668 |
| with > 5% ab initio | 0 | 0 | 0 | 0 | 0 |
| partial | 0 | 0 | 15 | 11 | 11 |
| with filled gap(s) | 0 | 0 | 0 | 0 | 0 |
| placed on multiple assembly-units | na | na | na | na | na |
| known RefSeq (NR_) | 1,593 | 1,587 | 125 | 163 | 1,544 |
| model RefSeq (XR_) | 163 | 133 | 5 | 25 | 141 |
| CDSs | 136,772 | 130,833 | 5,794 | 4,641 | 130,050 |
| fully-supported | 132,914 | 127,691 | 5,352 | 4,403 | 124,799 |
| with > 5% ab initio | 2,033 | 1,789 | 138 | 106 | 2,065 |
| partial | 521 | 390 | 389 | 277 | 417 |
| with major correction(s) | 47 | 105 | 41 | 126 | 268 |
| known RefSeq (NP_) | 67,116 | 66,976 | 2,106 | 2,543 | 66,970 |
| model RefSeq (XP_) | 69,078 | 63,466 | 3,524 | 2,075 | 62,692 |
Detailed reports
The counts below do not include pseudogenes.
BUSCO analysis of gene annotation
BUSCO v4.1.4 was run
in "protein" mode on the annotated gene set picking one longest protein per
gene, and run using the primates_odb10 lineage dataset. Results
are reported for the gene set from the primary assembly unit, and presented in BUSCO
notation.
References
- RefSeq: Pruitt KD, Brown
GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum
MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD,
Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M,
Kitts P, Maglott DR, Murphy TD, Ostell JM. Nucleic Acids Research 2014,
42(Database issue):D756-63
- BUSCO: Manni M, Berkeley MR, Seppey M, Simão FA,
Zdobnov EM. Molecular biology and evolution 2021.38(10):4647-4654
- RepeatMasker: Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0.
1996–2004. http://www.repeatmasker.org
- WindowMasker:
Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Bioinformatics 2006, 2:134-41
- Splign: Kapustin Y, Souvorov A, Tatusova T, Lipman D. Biology
Direct 2008, 3:20
- STAR:
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.
Bioinformatics 2013 Jan 1;29(1):15-21.
- Minimap2: Li H. Bioinformatics 2018 Sep 15;34(18):3094-3100
Gene and transcribed and non-transcribed
pseudogene features
Features annotated on more than one
assembly-unit.
This value is only provided if statistics are calculated on more
than one assembly-unit.
For more details on the assembly model see
https://www.ncbi.nlm.nih.gov/assembly/model/Features supported only partially by
experimental evidence,
for which more than 5% of their length was predicted by
Gnomon using a hidden Markov model
Coding transcripts predicted by
Gnomon with insertions, deletions or frameshifts relative to the genome
but a
strong hit to a SwissProt protein. Protein titles for these models are prefixed with
PREDICTED: LOW QUALITY PROTEIN
misc_RNA, tRNA, rRNA and ncRNA of all
classes. Does not include pseudogenes
Transcript features of transcribed
pseudogenes
Non-coding transcripts (misc_RNA,
lncRNA, rRNA, snRNA, snoRNA and guide_RNA)
predicted by Gnomon or RFAM and
cmsearch and assigned XR_* accessions
Long reads retrieved from the
Sequence Read Archive, such as 454 sequences generated with GS FLX instruments.
Transcripts for which less than
95% of the CDS aligns to the genomic sequence.
Usually indicate an assembly
problem.
Proteins predicted by Gnomon and
assigned XP_* accessions.
Proteins predicted by Gnomon with
insertions, deletions or frameshifts relative to the genome
but a strong hit to
a SwissProt protein. Titles for these proteins are prefixed with
PREDICTED: LOW
QUALITY PROTEIN.
Single-exon mRNAs, misc_RNAs and
ncRNAs of class lncRNA.
Does not include tRNAs, rRNAs or ncRNAs of class other
than lncRNA.
Exons in mRNAs, misc_RNAs and ncRNAs of class
lncRNA.
Does not include tRNAs, rRNAs or ncRNAs of class other than lncRNA.
Exons shared by multiple transcripts are counted once.
Exons in mRNA transcripts.
Exons
shared by multiple coding transcripts are counted once.
Exons in misc_RNAs and ncRNAs of class
lncRNA.
Exons shared by multiple non-coding transcripts are counted once.
Introns in mRNAs, misc_RNAs, and ncRNAs of
class lncRNA.
Does not include tRNAs, rRNAs or ncRNAs of class other than
lncRNA.
Introns shared by multiple transcripts are counted once.
Introns in mRNA transcripts.
Introns
shared by multiple coding transcripts are counted once.
Introns in misc_RNAs and ncRNAs of
class lncRNA.
Introns shared by multiple non-coding transcripts are counted
once.
Excludes CDSs of immunoglobulin and
T-cell receptor genes
CDSs with correction for premature
stop-codons, frameshifts or internal gaps
Model RefSeqs extended using transcript
sequence to compensate for an assembly gap
Genes with perfect match in exon
boundaries
Highly similar genes, with support
scores of 0.66 or more
(on a scale of 0 to 1) on both sides of the
comparison.
The support score is derived from a combination
of matching
exon boundaries and sequence overlap.
Corresponds to the Similar category in
the full report
Genes with support scores lower than
0.66 (on a scale of 0 to 1)
on one or both sides of the comparison, and genes
with changed
biotype or changed completeness, and split or moved genes.
Corresponds to categories Changed substantially, Changed locus
type,
Split, Moved, and Changed completeness in the full report
Novel genes or genes without a match
in the previous release.
Corresponds to categories Current-novel,
Current-other, and
Current-unmapped in the full report
Deprecated genes or genes
without a match in the current
release. Corresponds to categories
Previous-novel,
Previous-other, Previous-unmapped, and Merged in the full
report
Other changes