RetrogeneDB ID: | retro_ptro_2653 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 7:129396741..129397360(-) | ||
| Located in intron of: | ENSPTRG00000023911 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CD2BP2 | ||
| Ensembl ID: | ENSPTRG00000007995 | ||
| Aliases: | None | ||
| Description: | CD2 (cytoplasmic tail) binding protein 2 [Source:HGNC Symbol;Acc:1656] |
Retrocopy-Parental alignment summary:
>retro_ptro_2653
CGCCAGGCCTCAGACTTGGAAGAGGAGGACAGCTTGGGCCAGACCCCAGTGAGTGCCCAAGCCTTCTTGGAGGGACTTTT
GGAGCTCCTATTGCCTAGAGAGACAGTGGCTAGGGCACTGAGGCATCTGGGGGCCCGAGGAGGAGGCAAAGGGAGCAGCA
AGGGGCCTGGGTGACCCAGTTCCCTGCAGTGCCCGGACCGGCTCTCCGAATTGGCCGACCAGATGGTGGCCCAGGGAAAC
CTTGGCATGTACCAGGAAACGGAACAGTTGGCCATGCGGCTGAAGGGTTTGGGGTGCCAGGCCCTAGGGACCCCACAATC
CCACACCCCCACACTCCCTAGACATGTTCGCTGAGGAAGTGGCAGAGGGGGAACTGGAGACCCCAACCCCTACCCAGAGA
GGAGAAGCAGAGTTGCCAGGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGAGAACCCGGGGGATGCCGAGCT
GCATGGGCCCTTCACCAGCGACCAGATGCAGATCTGGGTGAGCGAAGGCTACTTTCCTGATGGTGTTTACTGCCGGAAGC
TGGACCCCCTTCATGGTCAGTTCTACAACTCCAAACGCATTGACTTTGACCTCTACACC
ORF - retro_ptro_2653 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.73 % |
| Parental protein coverage: | 67.1 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RQASDSEEEDSLGQTSMSAQALLEGLLELLLPRETVAGALRRLGARGGGKGS-KGPGQPSSPQRLDRLSG |
| RQASD.EEEDSLGQT..SAQA.LEGLLELLLPRETVA.ALR.LGARGGGKGS.KGPG.PSS.Q..DRLS. | |
| Retrocopy | RQASDLEEEDSLGQTPVSAQAFLEGLLELLLPRETVARALRHLGARGGGKGSSKGPG*PSSLQCPDRLSE |
| Parental | LADQMVARGNLGVYQETRERLAMRLKGLGCQTV-GPHNPTPLPSLDMFAEEVAEEELETPTPTQRGEAES |
| LADQMVA.GNLG.YQET.E.LAMRLKGLGCQ...G..........DMFAEEVAE.ELETPTPTQRGEAE. | |
| Retrocopy | LADQMVAQGNLGMYQET-EQLAMRLKGLGCQAL>GXXXXXXXXXXDMFAEEVAEGELETPTPTQRGEAEL |
| Parental | RGDGLVDVMWEYKWENTGDAELYGPFTSTQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT |
| .GDGLVDVMWEYKWEN.GDAEL.GPFTS.QMQ.WVSEGYFPDGVYCRKLDP..GQFYNSKRIDFDLYT | |
| Retrocopy | PGDGLVDVMWEYKWENPGDAELHGPFTSDQMQIWVSEGYFPDGVYCRKLDPLHGQFYNSKRIDFDLYT |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .05 RPM | 65 .19 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 66 .28 RPM |
| SRP007412_heart | 0 .00 RPM | 30 .69 RPM |
| SRP007412_kidney | 0 .03 RPM | 67 .86 RPM |
| SRP007412_liver | 0 .00 RPM | 80 .46 RPM |
| SRP007412_testis | 0 .11 RPM | 65 .76 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2653 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2653 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2653 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3900 |
| Gorilla gorilla | retro_ggor_2627 |
| Pongo abelii | retro_pabe_3179 |
| Macaca mulatta | retro_mmul_1735 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000169217 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000014271 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000021844 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000015767 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000007267 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000007995 | 1 retrocopy |
retro_ptro_2653 ,
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