RetrogeneDB ID: | retro_pabe_2259 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 3:135888248..135888826(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAF1 | ||
| Ensembl ID: | ENSPPYG00000018963 | ||
| Aliases: | None | ||
| Description: | MAF1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24966] |
Retrocopy-Parental alignment summary:
>retro_pabe_2259
TCAGGCCTCAGCCCCAGCAGCCTGATCAAGAACCAAGGTGGCAAGGACGAGGGCCCCCTCAGGTACAAGTGCAATTGCAA
GACCCTCTTCCACTTGATTGTCATGCTCAGCGAGTCCTTTCAGGCCTGACTATAACCTCAGCACAGCCCGCAGCCATGGG
TTCAGCTGGAAGCCCAGCCTCAGCTGGGTGGTGAACGCAGTCAACTGCAGTCTGTTCTCAGCTGCGTGGGGGAACATCAA
GGTCCGAGAACACAGCTGCGGAACACAGTGGATGAGGAGATCCGCCTGGCTTAATGGGACACCTACAGCTATAACCCAGA
CATGGACCCAGACCCCTTCAGGGAAGAAGACACCCTCTGGTCCTTCAACTACTTCTTCTACAACAAAGGGCTCAAGCAAA
TTTTCTTCTTCAGCCACCGCTCCATTAGCAGCTCCACCTGCACACCCTTAGAGGCAGGCAACGAGATGGACCTGGAACTG
GGTGAAGAGGAGGAAGAGAAAGAAAGCAGAGGCAGAGGCAGTGAGGGTGGGGCCAAAGAGACCAGACCATGGAGGACAGG
TTCCCAGTGATTTGTATG
ORF - retro_pabe_2259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.53 % |
| Parental protein coverage: | 75.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SGLSPSRLSKSQGGEEEGPLSDKCSRKTLFYLIATLNESF-RPDYDFSTARSHEFSREPSLSWVVNAVNC |
| SGLSPS.L.K.QGG..EGPL..KC..KTLF.LI..L.ESF.RPDY..STARSH.FS..PSLSWVVNAVNC | |
| Retrocopy | SGLSPSSLIKNQGGKDEGPLRYKCNCKTLFHLIVMLSESF>RPDYNLSTARSHGFSWKPSLSWVVNAVNC |
| Parental | SLFSAVREDFKAL-KPQLWNAVDEEICLAECDIYSYNPDLDSDPFGEDGSLWSFNYFFYNKRLKRIVFFS |
| SLFSA.....K.....QL.N.VDEEI.LA..D.YSYNPD.D.DPF.E...LWSFNYFFYNK.LK.I.FFS | |
| Retrocopy | SLFSAAWGNIKVR<RTQLRNTVDEEIRLA*WDTYSYNPDMDPDPFREEDTLWSFNYFFYNKGLKQIFFFS |
| Parental | CRSISGSTYTPSEAGNELDMELGEEEVEEESRSGGS--GAEET-STMEEDRVPVICI |
| .RSIS.ST.TP.EAGNE.D.ELGEEE.E.ESR..GS..GA.ET..TM.EDR.PVIC. | |
| Retrocopy | HRSISSSTCTPLEAGNEMDLELGEEEEEKESRGRGSEGGAKET<QTM-EDRFPVICM |
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 | 29 .91 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 23 .83 RPM |
| SRP007412_heart | 0 .00 RPM | 31 .94 RPM |
| SRP007412_kidney | 0 .00 RPM | 43 .06 RPM |
| SRP007412_liver | 0 .00 RPM | 16 .40 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2259 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2259 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2259 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2708 |
| Pan troglodytes | retro_ptro_1829 |
| Macaca mulatta | retro_mmul_1537 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000021450 | 1 retrocopy | |
| Homo sapiens | ENSG00000179632 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000007155 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000010478 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000018963 | 1 retrocopy |
retro_pabe_2259 ,
|
| Pan troglodytes | ENSPTRG00000020681 | 1 retrocopy |