RetrogeneDB ID: | retro_pabe_814 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:7896913..7898659(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TBCCD1 | ||
| Ensembl ID: | ENSPPYG00000014379 | ||
| Aliases: | None | ||
| Description: | TBCC domain containing 1 [Source:HGNC Symbol;Acc:25546] |
Retrocopy-Parental alignment summary:
>retro_pabe_814
GAAGTGTGGCGGTGCGGCGCCTGCATTAGCAGGTATGCAAAGAAGCCTTTTCACCCAGATGTCCTTAGAGATAATATGGA
TCAGTCCAGAGTTCTCCTCTGGGTGAAAGCAGAACCCTTTATAGTGGGTGCCTTGCAGGTCCCCCCTCCATCCAAGTTTA
GTCTTCACTATCTCAGGAAGATATCCACCTATGTGCAAATCCGGGCCACAGAAGGAGCTTACCTGCACCTCTACTGGTCT
ACATGGAGGCACATCACTTGTGGGAAGCTGCAGTTGGCCAAGGACCTGGCGTGGCTTTACTTCGAAATATTTGATAGTCT
TTCAGTGGAGACACCTGAGGAGCACCTGGAATGGTCTGAGGTTCTGTCCAACTGCATGTCTGAGGAGGAAGTTGAAAAGC
AGAGAAATCAGCTTTCAGTGGACACGCTACAGTTTCTGCTCTTCTTATACATTCAAGAGTTGAACAAGGTCTCCCTAAGG
ACATCTTTGATTGGCGAAGAGTGGCCCAGTCCCAGAAACAGATCTCGGTCTCCTGACCTGACTGTAAAATCTAATTGTCA
TAATAAGAACTGGAATGATTACAGTCACCAAGCTTTTGTCTATGATCATCTGTCTGATCTCCTCGAGCTGCTTTTAGATC
CAGAACAACTCACTGCATCATTTCATTCAACCCATAGTAGTCTAGTGTCCCGAGAAGCTGTTGTGGTGCTCAGCTTCCTT
ACTGAAGGTACAATAAGTAGAGCCAGGAAGATCTATCCACTTCATGAACTTGCACTGTGGCAGCCACTGCATGCAGATAG
TGGCTTCTCGAAGATCTCTAAGACTTTCTCTTTCTACAAACCGGAAACCTGGTTGAGGTCCTGTTTGACTGGGAATCCAT
TTGGTACATCAGCTTGCCTCAAGTCTGGAAAGAAATTGGCTTGGGCTCATCAAGTTGAAGGGACCACCAAAAGAGCTAAG
ATTGCTTGTAATACTCATGTGGCCCCTAGGATGCACCAACTGGTAGTGATGAGCCAGGTTTACAAGCAGACACTGGCTAA
GAGCTCAGATACTCTGGTGGGAGCACATGTAAAGATTCATCATTGCAACGAATCTTTTATATATCTGCTCTCTCCCTTAT
GATCTGTAACAATTGAGAAGTGAAGGAATAGCATCTTTGTCTTGGGCCCTGTAGGGACTACACTTCACCTCCACAGTTGT
GACAATGTTAAAGTCATTGCTGTTTGCCATCGTTTGTCCATCTTTTCTACAGCAGGTTGCATCTGTCACATTCTGATGCC
TATGCGCCCACTTATTCTCTCTGGGAACCAAACAGTAACTTTTGCCCCTTTTCATACCCATTACCCAATGCTAGAGGACC
ATACGGCCAGGACTGGCCTTGCTACAGTGCCTAACTATTGGGATAATCCAATGGTTGTGTGCAGAGAGAACAGTGACACC
AGTGTCTTCCGGCTTTTACCACCTTGTGAATTCTATGTATTTATTATTCCCTTTGAAATGGAAGGGGACACAACAGAGAT
ACCCGGAGGTCTTCCATCTGTATATCAGAAAGCACTGGGTCAAAGAGAACAGAAGATACAGATCTGGCAGAAAACTGTAA
AGGAGGCTCATTTGACAAAGGATCAAAGGAAGCAGTTCCAGGTACTGGTAGAGAACAAGTTTTATGAATGGTTGATTAAT
ACAGGACATCACCAACAGCTGGACAGCCTTGTACCCCCTGCAGCAGGCTCCAAACAAGCAGCTGGA
ORF - retro_pabe_814 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.19 % |
| Parental protein coverage: | 98.15 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EVRRSGPCISRYAKKPFHPDVLRDNMDQSRVLLWVKAEPFIVGALQVPPPSKFSLHYLRKISTYVKIRAT |
| EV.R.G.CISRYAKKPFHPDVLRDNMDQSRVLLWVKAEPFIVGALQVPPPSKFSLHYLRKISTYV.IRAT | |
| Retrocopy | EVWRCGACISRYAKKPFHPDVLRDNMDQSRVLLWVKAEPFIVGALQVPPPSKFSLHYLRKISTYVQIRAT |
| Parental | EGAYPRLYWSTWRHIACGKLQLAKDLAWLYFEIFDSLSVKTPEERLEWSEVLSNCMSEEEVEKQRNQLSV |
| EGAY..LYWSTWRHI.CGKLQLAKDLAWLYFEIFDSLSV.TPEE.LEWSEVLSNCMSEEEVEKQRNQLSV | |
| Retrocopy | EGAYLHLYWSTWRHITCGKLQLAKDLAWLYFEIFDSLSVETPEEHLEWSEVLSNCMSEEEVEKQRNQLSV |
| Parental | DTLQFLLFLYIQQLNKVSLRTSLIGEEWPSPRNRSQSPDLTEKSNCHNKNWNDYSHQAFVCDHLSDLLEL |
| DTLQFLLFLYIQ.LNKVSLRTSLIGEEWPSPRNRS.SPDLT.KSNCHNKNWNDYSHQAFV.DHLSDLLEL | |
| Retrocopy | DTLQFLLFLYIQELNKVSLRTSLIGEEWPSPRNRSRSPDLTVKSNCHNKNWNDYSHQAFVYDHLSDLLEL |
| Parental | LLDPEQLTASFHSTHSSLVSREAVVALSFLIEGTISRARKIYPLHELALWQPLHADSGFSKISKTFSFYK |
| LLDPEQLTASFHSTHSSLVSREAVV.LSFL.EGTISRARKIYPLHELALWQPLHADSGFSKISKTFSFYK | |
| Retrocopy | LLDPEQLTASFHSTHSSLVSREAVVVLSFLTEGTISRARKIYPLHELALWQPLHADSGFSKISKTFSFYK |
| Parental | LETWLRSCLTGNPFGTSACLKSGKKLAWAHQVEGTTKRAKIACNTHVAPRMHRLVVMSQVYKQTLAKSSD |
| .ETWLRSCLTGNPFGTSACLKSGKKLAWAHQVEGTTKRAKIACNTHVAPRMH.LVVMSQVYKQTLAKSSD | |
| Retrocopy | PETWLRSCLTGNPFGTSACLKSGKKLAWAHQVEGTTKRAKIACNTHVAPRMHQLVVMSQVYKQTLAKSSD |
| Parental | TLVGAHVKIHRCNESFIYLLSPLRSVTIEKCRNSIFVLGPVGTTLHLHSCDNVKVIAVCHRLSISSTTAC |
| TLVGAHVKIH.CNESFIYLLSPL.SVTIEK.RNSIFVLGPVGTTLHLHSCDNVKVIAVCHRLSI.ST..C | |
| Retrocopy | TLVGAHVKIHHCNESFIYLLSPL*SVTIEK*RNSIFVLGPVGTTLHLHSCDNVKVIAVCHRLSIFSTAGC |
| Parental | IFHILTPTRPLILSGNQTVTFAPFHTHYPMLEDHMARTGLATVPNYWDNPMVVCRENSDTSVFRLLPPCE |
| I.HIL.P.RPLILSGNQTVTFAPFHTHYPMLEDH.ARTGLATVPNYWDNPMVVCRENSDTSVFRLLPPCE | |
| Retrocopy | ICHILMPMRPLILSGNQTVTFAPFHTHYPMLEDHTARTGLATVPNYWDNPMVVCRENSDTSVFRLLPPCE |
| Parental | FYVFIIPFEMEGDTTEIPGGLPSVYQKALGQREQKIQIWQKTVKEAHLTKDQRKQFQVLVENKFYEWLIN |
| FYVFIIPFEMEGDTTEIPGGLPSVYQKALGQREQKIQIWQKTVKEAHLTKDQRKQFQVLVENKFYEWLIN | |
| Retrocopy | FYVFIIPFEMEGDTTEIPGGLPSVYQKALGQREQKIQIWQKTVKEAHLTKDQRKQFQVLVENKFYEWLIN |
| Parental | TGHRQQLDSLVPPAAGSKQAAG |
| TGH.QQLDSLVPPAAGSKQAAG | |
| Retrocopy | TGHHQQLDSLVPPAAGSKQAAG |
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 .11 RPM | 5 .86 RPM |
| SRP007412_cerebellum | 0 .12 RPM | 14 .23 RPM |
| SRP007412_heart | 0 .09 RPM | 3 .49 RPM |
| SRP007412_kidney | 0 .03 RPM | 6 .20 RPM |
| SRP007412_liver | 0 .21 RPM | 6 .43 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_814 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_814 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_814 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_954 |
| Pan troglodytes | retro_ptro_661 |
| Macaca mulatta | retro_mmul_784 |
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000014379 | 1 retrocopy |
retro_pabe_814 ,
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