RetrogeneDB ID: | retro_pabe_2742 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 5:62307815..62308895(-) | ||
| Located in intron of: | ENSPPYG00000015490 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GNL3L | ||
| Ensembl ID: | ENSPPYG00000020383 | ||
| Aliases: | None | ||
| Description: | guanine nucleotide binding protein-like 3 (nucleolar)-like [Source:HGNC Symbol;Acc:25553] |
Retrocopy-Parental alignment summary:
>retro_pabe_2742
GCTTTCAAGGCCAGGACCCAGCATCAGGTCAGCTTTGGAGCTGAAAACCTCACAAAGGTTCGGGAGAACTATTGCTGCCT
TGGTGAAGTGTGCACCCACATCCATATGGGCGTTGTGGGCCTTCCCAATATTGGGAAGAGCAGCCTGATTAAAAGCCTGA
AGTGCAGCCATGCATGCAGTGTGGGAGCCATTCCTGGGGTCACAAAATTCATGCAGGAGGTCCACCTGGACAAGTTCATC
TGGCTGCTGGATGCTCCAGCCATTGTTCCAGGGCCCAGCTCAGAGATGGGCACCATCCTGCATAACTGCATCCACATCTA
GAGGCTGGCAGACCCCATGACCCCAGTGGAGACCATCTTGCAGTGCTGCAACCTGGAGGAGATTTCCAACTATTACCTTC
TCTCTGGGTACCAGACTACTGAGCACTTTCTGATGGCAGTGGCCCACCATTTGGGGAAGAAGAGAGACTTACACAGTCAG
GCGCAGGCAGCCAAAGCTGTCCTAGATGACTGGGTGAGCGGGAAGATCAGCTTCTATAGACCACCACCACCCACTCACAC
TCTGCCCGCCCATCTCAGTGCTGAGATAATTAAGGAAATGACCAAGGTCTTTGACATCGAGGATACCGAGCAGGTCAATG
AAGACACCATGGAATGCTTGGCCACTGGAGAATCTGATGAGCTGTTGGGTGACACAGACCCACTCAAAATGGAGATCAAG
TTGCTCCATTCTCCGATGATGAAAATAGCAGATGCCATTGAAGATAAAGCTACTGTGTATAAGATTGGAGATCTCACTGG
TTATTGCACCAATCCGAATCATCATCAGATGGGGTGGGCTAAACTCAATGTAGACCACCACCCTAAAAAAAACAGTAAGG
TGGATGTGTGCCCAGTGGACTGCTGCCCAGTACTGCAGAGGATGATGGAAATGGACCCCCTACAACAGGGCCAGGCTCTG
GCATCCTCCCTGAAGAATAAGAATTTGCAGAAATGTGCAGATAAAATCCCCAGGGAGCTGTCTGATTCCATGATGTCTGC
TCTCCACCTCTCTGGCAATGCTGATGGCAGTGTTGGTGAC
ORF - retro_pabe_2742 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.86 % |
| Parental protein coverage: | 70.35 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ASESLLKSKACFGAENLMRVLGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACGVGAVPGITKF |
| A..........FGAENL..V..NYC.LGEV.THI..GVVGLPN.GKSSLI.SLK.S.AC.VGA.PG.TKF | |
| Retrocopy | AFKARTQHQVSFGAENLTKVRENYCCLGEVCTHIHMGVVGLPNIGKSSLIKSLKCSHACSVGAIPGVTKF |
| Parental | MQEVYLDKFIRLLDAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNYYGVSGFQTT |
| MQEV.LDKFI.LLDAP.IVPGP.SE.GTIL.NC.H...LADP.TPVETILQ.CNLEEISNYY..SG.QTT | |
| Retrocopy | MQEVHLDKFIWLLDAPAIVPGPSSEMGTILHNCIHI*RLADPMTPVETILQCCNLEEISNYYLLSGYQTT |
| Parental | EHFLTAVAHRLGKKKKGGLYSQEQAAKAVLADWVSGKISFYIPPPATHTLPTHLSAEIVKEMTEVFDIED |
| EHFL.AVAH.LGKK....L.SQ.QAAKAVL.DWVSGKISFY.PPP.THTLP.HLSAEI.KEMT.VFDIED | |
| Retrocopy | EHFLMAVAHHLGKKRD--LHSQAQAAKAVLDDWVSGKISFYRPPPPTHTLPAHLSAEIIKEMTKVFDIED |
| Parental | IEQANEDTMECLATGESDELLGDTDRLEMEIKLLHSPMTKIADAIENKTTVYKIGDLTGYCTNPNHHQMG |
| .EQ.NEDTMECLATGESDELLGDTD.L.MEIKLLHSPM.KIADAIE.K.TVYKIGDLTGYCTNPNHHQMG | |
| Retrocopy | TEQVNEDTMECLATGESDELLGDTDPLKMEIKLLHSPMMKIADAIEDKATVYKIGDLTGYCTNPNHHQMG |
| Parental | WAKRNVDHRPKSNNMVDVCSVDRRPVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSMMSA |
| WAK.NVDH.P.....VDVC.VD..PVLQR.ME.DPLQQGQALAS.LKN.K..QK.ADKI...LSDSMMSA | |
| Retrocopy | WAKLNVDHHPXXXSKVDVCPVDCCPVLQRMMEMDPLQQGQALASSLKN-KNLQKCADKIPRELSDSMMSA |
| Parental | LDLSGNADDGVGD |
| L.LSGNAD..VGD | |
| Retrocopy | LHLSGNADGSVGD |
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 .28 RPM | 4 .20 RPM |
| SRP007412_cerebellum | 0 .49 RPM | 7 .78 RPM |
| SRP007412_heart | 0 .18 RPM | 7 .19 RPM |
| SRP007412_kidney | 0 .07 RPM | 9 .18 RPM |
| SRP007412_liver | 0 .06 RPM | 5 .36 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2742 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2742 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2742 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3327 |
| Gorilla gorilla | retro_ggor_1296 |
| Macaca mulatta | retro_mmul_2084 |
| Callithrix jacchus | retro_cjac_1853 |
Parental genes homology:
Parental genes homology involve 8 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000252 | 2 retrocopies | |
| Homo sapiens | ENSG00000130119 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000007550 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000010144 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000008231 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000016233 | 1 retrocopy | |
| Oryzias latipes | ENSORLG00000014117 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020383 | 1 retrocopy |
retro_pabe_2742 ,
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