RetrogeneDB ID: | retro_pabe_3179 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 7:124916392..124917014(-) | ||
| Located in intron of: | ENSPPYG00000017972 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CD2BP2 | ||
| Ensembl ID: | ENSPPYG00000007267 | ||
| Aliases: | None | ||
| Description: | CD2 antigen cytoplasmic tail-binding protein 2 [Source:RefSeq peptide;Acc:NP_001125729] |
Retrocopy-Parental alignment summary:
>retro_pabe_3179
CGCCAGGCCTCAGACTTGGAAGAGGAGGACAGCTTGGGCCAGACCCCAGTGAGTGCCCAAGCCCTCTTGGAGGGACTTTT
GGAGCTCCTATTGCCTAGAGAGACAGTGGCTACGGCACTGAGGTGTCTGGGGGCCCGACGAGGAGGCAAAGGGAGCAGCA
AGGGGCCTGGGTGACCCAGTTCCCCGCAGCGCCCGGACCGGCTCTCCGAACTGGCCGACCAGATGGTGGCCCAGGGAAAC
CTTGGCATGTACCAGGAAACAAGGGAACAGTTGGCCATGTGGCTGAAGGGTTTGGGGTGCCAGGCCCTAGGGACCCCACA
ATCCTACACCCCCACACTCCCTGGACATGTTTGCTGAGGAAGTGGCGGAGGGGGAACTGGTGACCCCAACCCCTACCCAG
AGAGGAGAAGCAGAGTTGCCAGGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGAGAACCCGGGGGATGCTGA
GCTGCATGGGCCCTTCAACAGCACCCAGATGCAGATCTGGGTGAGTGAAGGCTACTTTCCTGATGGTGTTTATTGCTGGA
AGCTGGACCCCCTTAGTGGTCAGTTCTACAACTCCAAACGCATTGACTTTGACCTCTACACC
ORF - retro_pabe_3179 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.33 % |
| Parental protein coverage: | 59.94 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RQASDSEEEDSLGQTPMSAQALLEGLLELLLPRETVAGALRRLGARGGGRG-SKGPGRPSSPQRLDRLSG |
| RQASD.EEEDSLGQTP.SAQALLEGLLELLLPRETVA.ALR.LGAR.GG.G.SKGPG.PSSPQR.DRLS. | |
| Retrocopy | RQASDLEEEDSLGQTPVSAQALLEGLLELLLPRETVATALRCLGARRGGKGSSKGPG*PSSPQRPDRLSE |
| Parental | LADQMVARGNLGVYQETRERLAMRL--LGCQTL--PHNPTPP-SLDMSLRRLAEEELETPTIKKRGEAES |
| LADQMVA.GNLG.YQETRE.LAM.L..LGCQ.L..P...TP..SLDM.....AE.EL.TPT...RGEAE. | |
| Retrocopy | LADQMVAQGNLGMYQETREQLAMWLKGLGCQALGTPQSYTPT>SLDMFAEEVAEGELVTPTPTQRGEAEL |
| Parental | PGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT |
| PGDGLVDVMWEYKWEN.GDAEL.GPF.S.QMQ.WVSEGYFPDGVYC.KLDP..GQFYNSKRIDFDLYT | |
| Retrocopy | PGDGLVDVMWEYKWENPGDAELHGPFNSTQMQIWVSEGYFPDGVYCWKLDPLSGQFYNSKRIDFDLYT |
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 .06 RPM | 86 .14 RPM |
| SRP007412_cerebellum | 0 .12 RPM | 53 .75 RPM |
| SRP007412_heart | 0 .18 RPM | 35 .16 RPM |
| SRP007412_kidney | 0 .17 RPM | 89 .26 RPM |
| SRP007412_liver | 0 .18 RPM | 37 .70 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3179 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3179 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3179 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3900 |
| Pan troglodytes | retro_ptro_2653 |
| Gorilla gorilla | retro_ggor_2627 |
| 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 |
retro_pabe_3179 ,
|
| Pan troglodytes | ENSPTRG00000007995 | 1 retrocopy |