RetrogeneDB ID: | retro_pabe_3715 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:150152529..150153936(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NOL11 | ||
| Ensembl ID: | ENSPPYG00000008567 | ||
| Aliases: | None | ||
| Description: | nucleolar protein 11 [Source:RefSeq peptide;Acc:NP_001125582] |
Retrocopy-Parental alignment summary:
>retro_pabe_3715
TTGCTTAAGGCTGTTGTGTCTGGTAACACTTGAAATGGAGTTACACTCACTGCGCTGGATCAGGATCACGTCACAGTCCT
GGGAAGTCCACTAGCAGCTTCTAAGGAATGCCTCTCTGTATGGAACATAAAATTTCAAACACTACAGACTTCAAAAGAGT
TACCACAAGGGACCAGTGGTCAACTCTGGTATTATGGGGAAAATTTGTTTATGCTATGTGGAAAATCTCTAACTGTGATT
CCATACAACTGTGAAGTGTCATCATTAGCAGGTGCTCATGGAAAACTCAAGCATAGTCAAGATCCAGGAACTCATGTCGT
GCCCCATTTTGTAAACTGGGAAACACCTCAAGGATGTGGACTTGGGTCCCAGAACTCAGAGCAGTCAAGAAGAATTTTAA
GGAGATGAAAAATTGAAGTGAGTTTACAGCCAGAGGTATCACCATCCAAACAACTTTTGTCAACCATAATGAAAGATTCA
GAGAAACACACTGAAGTAGAAGTATGGAAATTTTTGGCTCTGAAGCAGACCCCTGACTTTCATACTGTCAATGGGGACAC
AGTAACAGGACTTCTGGAAAGATGTAAAGCAGAACCATCATTTTATCCCCAGAACTGTCTGATGCAGCTTATCCAAATGC
ATGTGCTTTCTTACAGTTTGTGCCCTGACTTAATGGAGATTGCCTTAAAAAAGAAAGATGTACAGTTGTTACAACTCTGT
CTACAGCAGTTCCCTGACATTCCTGAATCAGTCACCTGTGCTTGCTTAAAAATTTTCTTGAGAATTGGTGATGACAGTCT
TCAAGAAACAGATGTCAGTATGGAGTCAGTTTTTGACTATAGTAATTCTGTACATGATGAGAAAATGGAAGAGCAAACTG
GAATTCTTCAAAATGGCTTCAATCCTGAAGAAGATAAATACAATAACTGTGATCAAGAGTTAAATAAAAAGCCCCAGGAC
AAAACCAAGGAGACCATTTCATGCTCTGTGATACCAAAAAGAGCAGCTCTACTTAATGCAATTCTTCATTCAGCATATAG
CGAAACATTTCTTCTGCCTCATTTGAAAAACATCCCAGCACAGCATATCACACTGTTTCTCAAGTATTTGTGTTTCCTTT
ATCTGAAGTGTAGCGAAAATGCTACTATGACTCTTCCTGGAATACACCCACCTACCTTGAACCAGATTATGGATTGGATA
TGTCTACTTCTGGATGCAAATTTTACTGTTGTAGTAATGATGCCAGAAGCAAAGAGGCTATTGATAAATCTTTACAAGCT
TGTAAAATCTCTGATATCTGTTTATTCCGAGCTCAACAAGATTGAAGTAAGTTTTTGGGAGCTACAGAAATTAAATCAAG
AAAAGAATAATAGAGGATTATATTCAATTGAGGTGCTGGAGCTCTTC
ORF - retro_pabe_3715 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.96 % |
| Parental protein coverage: | 65.32 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LLKAVVSDNTQNGVALTALDQDHVAVLGSPLAASKECLSVWNIKFQTLQTSKELSQGTSGQVWYYGEHLF |
| LLKAVVS.NT.NGV.LTALDQDHV.VLGSPLAASKECLSVWNIKFQTLQTSKEL.QGTSGQ.WYYGE.LF | |
| Retrocopy | LLKAVVSGNT*NGVTLTALDQDHVTVLGSPLAASKECLSVWNIKFQTLQTSKELPQGTSGQLWYYGENLF |
| Parental | MLHGKSLTVIPYKCEVSSLAGALGKLKHSQDPGTHVVPHFVNWETPQGCGLGFQNSEQSRRILRRRKIEV |
| ML.GKSLTVIPY.CEVSSLAGA.GKLKHSQDPGTHVVPHFVNWETPQGCGLG.QNSEQSRRILRR.KIEV | |
| Retrocopy | MLCGKSLTVIPYNCEVSSLAGAHGKLKHSQDPGTHVVPHFVNWETPQGCGLGSQNSEQSRRILRR*KIEV |
| Parental | SLQPEVPPSKQLLSTIMKDSEKHIEVEVRKFLALKQTPDFHTVVGDTVTGLLERCKAEPSFYPRNCLMQL |
| SLQPEV.PSKQLLSTIMKDSEKH.EVEV.KFLALKQTPDFHTV.GDTVTGLLERCKAEPSFYP.NCLMQL | |
| Retrocopy | SLQPEVSPSKQLLSTIMKDSEKHTEVEVWKFLALKQTPDFHTVNGDTVTGLLERCKAEPSFYPQNCLMQL |
| Parental | IQTHVLSYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFLSIGDDSLQETDVSMESVFDY |
| IQ.HVLSYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFL.IGDDSLQETDVSMESVFDY | |
| Retrocopy | IQMHVLSYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFLRIGDDSLQETDVSMESVFDY |
| Parental | SNSVHDEKMEEQTEILQNGFNPEEDKCNNCDQELNKKPQDETKESTSCPVVQKRAALLNAILHSAFSETF |
| SNSVHDEKMEEQT.ILQNGFNPEEDK.NNCDQELNKKPQD.TKE..SC.V..KRAALLNAILHSA.SETF | |
| Retrocopy | SNSVHDEKMEEQTGILQNGFNPEEDKYNNCDQELNKKPQDKTKETISCSVIPKRAALLNAILHSAYSETF |
| Parental | LLPHLKDIPAQHITLFLKYLYFLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRL |
| LLPHLK.IPAQHITLFLKYL.FLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRL | |
| Retrocopy | LLPHLKNIPAQHITLFLKYLCFLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRL |
| Parental | LINLYKLVKSQITVYSELNKIEVSFRELQKLNQEKNNRGLYSIEVLELF |
| LINLYKLVKS.I.VYSELNKIEVSF.ELQKLNQEKNNRGLYSIEVLELF | |
| Retrocopy | LINLYKLVKSLISVYSELNKIEVSFWELQKLNQEKNNRGLYSIEVLELF |
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 | 7 .52 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 20 .06 RPM |
| SRP007412_heart | 0 .06 RPM | 8 .13 RPM |
| SRP007412_kidney | 0 .00 RPM | 13 .39 RPM |
| SRP007412_liver | 0 .03 RPM | 14 .20 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3715 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3715 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3715 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4772 |
| Pan troglodytes | retro_ptro_3178 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000130935 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000001436 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000008567 | 1 retrocopy |
retro_pabe_3715 ,
|
| Pan troglodytes | ENSPTRG00000009566 | 1 retrocopy |