RetrogeneDB ID: | retro_ptro_3178 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | X:150923304..150924483(+) | ||
| 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: | ENSPTRG00000009566 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_3178
ATCTCTGTGATTCCATACAACTGTGAAGTGTCATCATTAGCAGGTGCTCATGGAAAACTCAAGCATAGTCAAGATCCAGG
AACTCATGTCGTGCCCCATTTTGTAAACTGGGAAACACCTCAAGGATGTGGACTTGGGTCCCAGAACTCAGAGCAGTCAA
GAAGAATTTTAAGGAGACGAAAAATTGAAGTGAGTTTACAGCCAGAGGTATCACCATCCAAACAACTTTTGTCAACCATA
ATGAAAGATTCAGAGAAACACACTGAAGTAGAAGTATGGAAATTTTTGGCTCTGAAGCAGACCCCTGACTTTCATACTGT
CACTGGGGACACAGTAACAGGACTTCTGGAAAGGTGTAAAGCAGAACCATCATTTTATCCCCGGAGCTGTCTGATGCACC
TTATCCAAGTGCATGTGCTTTCTTACAGTTTGTGCCGTGACTTAATGGAGATTGCCTTAAAAAAGAAAGATGTACAGTTG
TTACAACTCTGTCTACAGCAGTTCCCTGACATTCCTGAATCGGTCACCTGTGCTTGCTTAAAAATTTTCTTGAGAATTGG
TGATGACAGTATTCAAGAAACAGATGTCAGTATGGAGTCAGTTTTTGACTATAGTAATTCTGTACATGATGAGAAAATGG
AAGAGCAAACTGGAATTCTTCAAAATGGCTTCAATCCTGAAGAAGATAAATACAGTAACTGTGATCAAGAGTTAAATAAA
AAGCCCCAGGACAAGACAAAGGAGACCATTTCATGCTCTGTGATACCAAAAAGAGCAGCTCTACTTAATGCAATTCTTCA
TTCAGCATATAGCGAAACATTTCTTCTGCCTCATTTGAAAAACATCCCAGCACAGCATATCACACTGTTTCTCAAGTGTT
TGTGTTTCCTTTATCTGAAGTGTAGCGAAAATGCTACTATGACTCTTCCTGGAATACACCCACCTACCTTGAACCAGATT
ATGGATTGGATATGTCTACTTCTGGATGCAAATTTTACTGTTGTAGTAATGATGCCAGAAGCAAAGAGGCCACTGATAAA
TCTTTACAAGCTTGTAAAATCTCAGATATCTGTTTATTCCAAGCTCAACAAGATTGAAGTAAGTTTTTGGGAGCTACAGA
AATTAAATCAAGAAAAGAATAATAGAGGATTATATTCAATTGAAGTGCTGGAGCTCTTC
ORF - retro_ptro_3178 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.62 % |
| Parental protein coverage: | 54.8 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LTVIPYKCEVSSLAGALGKLKHSQDPGTHVVSHFVNWETPQGCGLGFQNSEQSRRILRRRKIEVSLQPEV |
| ..VIPY.CEVSSLAGA.GKLKHSQDPGTHVV.HFVNWETPQGCGLG.QNSEQSRRILRRRKIEVSLQPEV | |
| Retrocopy | ISVIPYNCEVSSLAGAHGKLKHSQDPGTHVVPHFVNWETPQGCGLGSQNSEQSRRILRRRKIEVSLQPEV |
| Parental | PPSKQLLSTIMKDSEKHIEVEVRKFLALKQTPDFHTVIGDTVTGLLERCKAEPSFYPRNCLMQLIQTHVL |
| .PSKQLLSTIMKDSEKH.EVEV.KFLALKQTPDFHTV.GDTVTGLLERCKAEPSFYPR.CLM.LIQ.HVL | |
| Retrocopy | SPSKQLLSTIMKDSEKHTEVEVWKFLALKQTPDFHTVTGDTVTGLLERCKAEPSFYPRSCLMHLIQVHVL |
| Parental | SYSLCPDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFLSIGDDSLQETDVNMESVFDYSINSVH |
| SYSLC.DLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFL.IGDDS.QETDV.MESVFDYS.NSVH | |
| Retrocopy | SYSLCRDLMEIALKKKDVQLLQLCLQQFPDIPESVTCACLKIFLRIGDDSIQETDVSMESVFDYS-NSVH |
| Parental | DEKMEEQTEILQNGFNPEEDKCNNCDQELNKKPQDETKESTSCPVVQKRAALLNAILHSAYSETFLLPHL |
| DEKMEEQT.ILQNGFNPEEDK..NCDQELNKKPQD.TKE..SC.V..KRAALLNAILHSAYSETFLLPHL | |
| Retrocopy | DEKMEEQTGILQNGFNPEEDKYSNCDQELNKKPQDKTKETISCSVIPKRAALLNAILHSAYSETFLLPHL |
| Parental | KDIPAQHITLFLKYLYFLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRLLINLY |
| K.IPAQHITLFLK.L.FLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKR.LINLY | |
| Retrocopy | KNIPAQHITLFLKCLCFLYLKCSENATMTLPGIHPPTLNQIMDWICLLLDANFTVVVMMPEAKRPLINLY |
| Parental | KLVKSQISVYSELNKIEVSFRELQKLNQEKNNRGLYSIEVLELF |
| KLVKSQISVYS.LNKIEVSF.ELQKLNQEKNNRGLYSIEVLELF | |
| Retrocopy | KLVKSQISVYSKLNKIEVSFWELQKLNQEKNNRGLYSIEVLELF |
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 .21 RPM | 11 .94 RPM |
| SRP007412_cerebellum | 0 .07 RPM | 18 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 11 .69 RPM |
| SRP007412_kidney | 0 .13 RPM | 20 .84 RPM |
| SRP007412_liver | 0 .00 RPM | 14 .04 RPM |
| SRP007412_testis | 0 .00 RPM | 12 .96 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3178 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3178 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_3178 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4772 |
| Pongo abelii | retro_pabe_3715 |
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 | |
| Pan troglodytes | ENSPTRG00000009566 | 1 retrocopy |
retro_ptro_3178 ,
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