RetrogeneDB ID: | retro_pabe_2898 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 6:107596177..107597309(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CHAF1B | ||
| Ensembl ID: | ENSPPYG00000011403 | ||
| Aliases: | None | ||
| Description: | chromatin assembly factor 1, subunit B (p60) [Source:HGNC Symbol;Acc:1911] |
Retrocopy-Parental alignment summary:
>retro_pabe_2898
CCTTTAGGTCAATATGTTGCTACTCTGAGCTGTGACAGGGTGCTGCGGGTATACAGTATACAGAAGAAGCATGTGGTTTT
TAATGTTTCAAAGATGCTATCTGGAATAGGGGCTGAAGGAGAGGCAAGAAGCTACAGGATGTTTCATGACAACAGCATGA
AGTTGTTCTTCCGTAGACTGAGTTTCACTCCTGATGGATCTTTGCTCCTCACACCAGCTGGATGTGTGGAATCTGGTGAA
AATGTAATGAACACCACTTACGTTTTCTCCAGGAAGAATCTTAAAAGGCCCATCGCTCATCTTCCATGTCCTGGAAAAGC
CACTCTTGCTGTTGGCAGCTGTCTGGTCTACTTTGAACTGAGGCCGGTGGTGGAAACAGGTGTGGAGCTAATGAGTCTGC
CCTACCGCCTGGTATTTGCTGTGGCTTAGGAGGACTCTGTGCTTCTGGACACCCAGGAATCCTTCCCTTTCGGTTACGTG
TCTAATATACATTACCACACCCTCAGTGACATTTCATGATCTAGCGATGGCGCCTTCATGGCCATTTCTTCCACAGACAG
TTACTGCTCGTTCGTGACATTTGAGAAAGGTGAACTTGGAATACTTTTAAAAGAGAAGTCAGTTTTGAGCACAAGAACTC
CTGATACAGCAAAGAAAACCAAGAGTCAGACACACCGAGGGTCTTTGCCAGGACCCAGACCAGTAGAGGGAACAACTGCC
AGCAGAACCCAAGATCCCAGCAACCCCTGCTCGACCCCCACTCAGGCCAGACAGGCCCCAGCCCCAGCAGCCATCAGGAA
CCCTCCCTCTATCATTCTGCTGTCAAAAGCTCCTTGCCGAGGCCTTCGGAGGAGAAGACCCTGCCGCCCAGTAGTTAAAA
CACAAAAGCCCACCCATCCCGGAGGGTCACTCTGAACACATTGCAATCCTGGAGCAAGACAATACCCTGGAGAATAAACT
TAATACCCTTAAAGACAGACACTCCACCAAAGTCTGTACCAATCAATGTAATTTCCACCCCTTCTGCAGAAGAATTTAGT
AAGAGATGCCTGGAAACACTCAGGGCAGTCCCGCAGAGCTAAAACAGCCCAGACTCAATGAAAACAAAGGGGGCACTGAA
AGTCTGGAACCT
ORF - retro_pabe_2898 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.3 % |
| Parental protein coverage: | 67.8 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PLGQYVATLSCDRVLRVYSIQKKRVAFNVSKMLSGIGAEGEARSYRMFHDDSMKSFFRRLSFTPDGSLLL |
| PLGQYVATLSCDRVLRVYSIQKK.V.FNVSKMLSGIGAEGEARSYRMFHD.SMK.FFRRLSFTPDGSLLL | |
| Retrocopy | PLGQYVATLSCDRVLRVYSIQKKHVVFNVSKMLSGIGAEGEARSYRMFHDNSMKLFFRRLSFTPDGSLLL |
| Parental | TPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVRCCPVYFELRPVVETGVELMSLPYRLVFA |
| TPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAV..C.VYFELRPVVETGVELMSLPYRLVFA | |
| Retrocopy | TPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVGSCLVYFELRPVVETGVELMSLPYRLVFA |
| Parental | VASEDSVLLYDTQQPFPFGYVSNIHYHTLSDISWSSDGAFLAISSTDGYCSFVTFEKDELGIPLKEKPVL |
| VA.EDSVLL.DTQ..FPFGYVSNIHYHTLSDIS.SSDGAF.AISSTD.YCSFVTFEK.ELGI.LKEK.VL | |
| Retrocopy | VA*EDSVLL-DTQESFPFGYVSNIHYHTLSDIS*SSDGAFMAISSTDSYCSFVTFEKGELGILLKEKSVL |
| Parental | SMRTPDTAKKTKSQTHRGSSPGPRPVEGTPASRTQDPSSPGTTPPQARQAPAPTAIRDPPSIT-PAVRSP |
| S.RTPDTAKKTKSQTHRGS.PGPRPVEGT.ASRTQDPS.P..TP.QARQAPAP.AIR.PPSI...AV.S. | |
| Retrocopy | STRTPDTAKKTKSQTHRGSLPGPRPVEGTTASRTQDPSNPCSTPTQARQAPAPAAIRNPPSII<SAVKSS |
| Parental | LPGPSEEKSLQPSSQNTKVHPSRRVTLNTLQAWSKTTPRRMNLTPLKTDTPPSSVPTSVISTPSTEEIQS |
| LP.PSEEK.L.PSS.NTK.HPSRRVTLNTLQ.WSKT.P.R.NL.PLKTDTPP.SVP..VISTPS.EE... | |
| Retrocopy | LPRPSEEKTLPPSS*NTKAHPSRRVTLNTLQSWSKTIPWRINLIPLKTDTPPKSVPINVISTPSAEEFSK |
| Parental | -ETPGDAQGSPPELKRPRLDENKGGTESLDP |
| .E.PG..QGSP.ELK.PRL.ENKGGTESL.P | |
| Retrocopy | <EMPGNTQGSPAELKQPRLNENKGGTESLEP |
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 .00 RPM | 7 .91 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 7 .78 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .78 RPM |
| SRP007412_kidney | 0 .00 RPM | 1 .56 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .80 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2898 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2898 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2898 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3504 |
| Pan troglodytes | retro_ptro_2375 |
| Gorilla gorilla | retro_ggor_2369 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000159259 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000015726 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000004429 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000011403 | 1 retrocopy |
retro_pabe_2898 ,
|
| Pan troglodytes | ENSPTRG00000013891 | 1 retrocopy |