RetrogeneDB ID: | retro_cjac_3909 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286228.1:4276..6260(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UBAP2L | ||
| Ensembl ID: | ENSCJAG00000009677 | ||
| Aliases: | None | ||
| Description: | ubiquitin associated protein 2-like [Source:HGNC Symbol;Acc:29877] |
Retrocopy-Parental alignment summary:
>retro_cjac_3909
GCATGGAGGACTGCAACAGAGGAATGGGGGACTGAAGATTGGAATGAAGATCTTTCTGAGACCAAGATCTTCACTGCCTC
TAATGTGTCTTCAGTGCCTCTGCCTGTGGAGAATGTGACAATCACTGCTGGTCAGAGAATTGACCTTGCTGTTCTTCTCG
GGAAGACACCATCTACAATGGAGAATGATTCATCTAATCTGGATCCATCTCAGGCTCCTTCTCTGGCCCAGCCTCTGGTG
TTCAGCAACTCAAAGCAGACTCCACAACACAGCCGGCTTCAGGGAACACATTTTCTCATCACAGTATGGTGAGCCTGCTG
GGGAAAGGATTTGGTGATGGTGAATGAAGCTAAAGGCGGCAGTACTACGGGCTCCCAGTTCTTGGAGCAATTCAAGACTG
CTCAAGCCCTGGCTCAGTTGGCAGTTCAGCATTCTTAGACTGGAAGCACCACCACCTCCTCTTGGGACATGGGCTTGATG
ACACAATCCCCATCATTGGTGTAGTATGATTTGAAGAACCCAAATGATTCAACAGTGCACAGCCCCTTTATAAAGCGCCA
GGCTTTTACCCCATCTTCAACCATGATGGAGGTGTTCCTTCAGGAGAAGTCACCTGCAGTGGCTACCTCCACAGCTGCAC
CTCCACCTCAGTCTTCTCCTCTGCCAAGGAAATCCACATCGGCTCCATCGATGTCACCTAGATCTTCAGACAACCAGTCC
TCTAGCCCTAGCCAGCTCAGAAAAAGCTGAAACAGCAGGAGAAAAAAGCCTCCTTGACTTCTAAGATTCCTGCTCTGGCT
GTGGAGATGCCTGGCTCAGCAGCTATCTCAGGGCTAAACCTGCAGTTTGGGGCATTGCAGTTTGGGTCAGAGCCAGTCCT
TTCTGATTATGAGTCCACCCCTACCACGAGCGCCTCTTCAAGCCAGCTCCAGTAGCCTATATACCAGCACGGCCAGCGAA
TCTTCATCTACAATTTGATCTAACCAGAGTCAGGAGTCGTTATCAGAGTGGCCCAATTCAGTCGACAACCTATACCTCCC
AAAATAATGCTCAGGGCCCTCTTTATGAACAGAGATCCACACAGACTCGGTGGTACCCCAGCTCCATCTTTTCATCACCC
CAAAAGGACCTGACTCAGGCAAAGAATGGCTTCAGTTCTGTGCAGGCCACACAATTACGGACCACTCAATCTGTTGAAGG
TGCTACAAGCTCTGCAGTAAAATCTGATTTACCCTCCACTTCTAGCATCCCCGCTCTCAATGAAATGGTATCTGCACCTT
CCTTAGTGACAACAACCAATCTGCACTCATCCTCCTTGGGTGGCTTGAGCCACAGTGAGGAGATTCGAAATACTAACACC
ACACAACACAGCAGCACATTATCTACGCAGCAGAATACCCTTTCGTCATCAACATCTTCTGGGCACACTTCAACATCCAC
TCTTTTGCACACAAGCATGGAGAGTGAAACGAATCTCTATTCTTCCTCCAGCACTTTTTCCACCACATCCAGCACAGTCT
CTGCACCTCCCCCAGTGGTCAGTGTCTCCTCCACTCTCAATAGTGGCAGTAGTCTGGGTCTCAGCCTAGGCTGCAACTCC
CCTGTCACAGCCTCGACTCGAAGTTCAGTTGCCACGACTTCAGGAAAAGCTCCTCCCAGCCTCCCTCCTGGGGTCCCACC
GTTGTTGCCTAATCCGTGTATTGTGGCTCCAGGGCTGTTACATGCCTATCCGCCACAAGTATATGGTTATGATGACTTGC
AGATGCTTCAAACAAGATTTCCATTGTATTACTACAGCATCCTATTTCCCACACTCACTACTCCGCTGACTGGGGGGGAT
GGTAGCCTGGCCGGCAACCCTTATTCTGGTGACCTCACAAAGTTCGGCCTTTGGGATGCCTCCTCCCCAGCCCCGGCCAC
AACCTTGGCCCAACCCCAACAGAACCAGACGCAGAATCACCACACCACGCAGCAGACATTCCTG
ORF - retro_cjac_3909 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.53 % |
| Parental protein coverage: | 61.17 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | AWRTATEEWGTEDWNEDLSETKIFTASNVSSVPLPAENVTITAGQRIDLAVLLGKTPSTMENDSSNLDPS |
| AWRTATEEWGTEDWNEDLSETKIFTASNVSSVPLP.ENVTITAGQRIDLAVLLGKTPSTMENDSSNLDPS | |
| Retrocopy | AWRTATEEWGTEDWNEDLSETKIFTASNVSSVPLPVENVTITAGQRIDLAVLLGKTPSTMENDSSNLDPS |
| Parental | QAPSLAQPLVFSNSKQT-AISQPASGNTFSHHSMVSMLGKGFGD-VGEAKGGSTTGSQFLEQFKTAQALA |
| QAPSLAQPLVFSNSKQT....QPASGNTFSHHSMVS.LGKGFGD.V.EAKGGSTTGSQFLEQFKTAQALA | |
| Retrocopy | QAPSLAQPLVFSNSKQT<STTQPASGNTFSHHSMVSLLGKGFGD>VNEAKGGSTTGSQFLEQFKTAQALA |
| Parental | QLAAQHSQSGSTTTSSWDMGSTTQSPSLVQYDLKNPNDSTVHSPFTKRQAFTPSSTMMEVFLQEKSPAVA |
| QLA.QHS..GSTTTSSWDMG..TQSPSLV.YDLKNPNDSTVHSPF.KRQAFTPSSTMMEVFLQEKSPAVA | |
| Retrocopy | QLAVQHS*TGSTTTSSWDMGLMTQSPSLV*YDLKNPNDSTVHSPFIKRQAFTPSSTMMEVFLQEKSPAVA |
| Parental | TSTAAPPPPSSPLPSKSTSAPQMSPGSSDNQSSSPQ-PAQQKLKQQKKKASLTSKIPALAVEMPGSADIS |
| TSTAAPPP.SSPLP.KSTSAP.MSP.SSDNQSSSP..PAQ.KLKQQ.KKASLTSKIPALAVEMPGSA.IS | |
| Retrocopy | TSTAAPPPQSSPLPRKSTSAPSMSPRSSDNQSSSPS<PAQKKLKQQEKKASLTSKIPALAVEMPGSAAIS |
| Parental | GLNLQFGALQFGSEPVLSDYESTPTTSASSSQ-AP-SSLYTSTASESSSTISSNQSQE-SGYQSGPIQST |
| GLNLQFGALQFGSEPVLSDYESTPTTSASSSQ.AP.SSLY.......SS..........S.YQSGPIQST | |
| Retrocopy | GLNLQFGALQFGSEPVLSDYESTPTTSASSSQ<AP<SSLY-TSTASESSSTI*SNQSQ>SRYQSGPIQST |
| Parental | TYTSQNNAQGPLYEQRSTQTRRYPNSISSSPQKDLTQAKANGAKKLEVVIGKLKKAHIFLGATGSAVKSD |
| TYTSQNNAQGPLYEQRSTQTR.YP.SI.SSPQKDLTQAK.NG..........L.......GAT.SAVKSD | |
| Retrocopy | TYTSQNNAQGPLYEQRSTQTRWYPSSIFSSPQKDLTQAK-NGFSSVQAT--QLRTTQSVEGATSSAVKSD |
| Parental | SPSTSSIPPLNETVSAASLLTTTNQHSSSLGGLSHSEEIPNTTATQHSSSVQATQLQTTQSVEVSESRCQ |
| .PSTSSIP.LNE.VSA.SL.TTTN.HSSSLGGLSHSEEI.NT..TQHSS....TQ.Q.T.S...S..... | |
| Retrocopy | LPSTSSIPALNEMVSAPSLVTTTNLHSSSLGGLSHSEEIRNTNTTQHSSTL-STQ-QNTLSSSTSSGHTS |
| Parental | LSPLKHTSVESEANLHSSSSTFSTTSSTVSAPPPVVSVSSSLNSGSSLGLSLGSNSTVTASTRSSVATTS |
| .S.L.HTS.ESE.NL.SSSSTFSTTSSTVSAPPPVVSVSS.LNSGSSLGLSLG.NS.VTASTRSSVATTS | |
| Retrocopy | TSTLLHTSMESETNLYSSSSTFSTTSSTVSAPPPVVSVSSTLNSGSSLGLSLGCNSPVTASTRSSVATTS |
| Parental | GKAPPNLPPGVPPLLPNPYIMAPGLLHAYPPQVYGYDDLQMLQTRFPLDYYSIPFPTPTTPLTGREGSLA |
| GKAPP.LPPGVPPLLPNP.I.APGLLHAYPPQVYGYDDLQMLQTRFPL.YYSI.FPT.TTPLTG..GSLA | |
| Retrocopy | GKAPPSLPPGVPPLLPNPCIVAPGLLHAYPPQVYGYDDLQMLQTRFPLYYYSILFPTLTTPLTGGDGSLA |
| Parental | SNPYSGDLTKFGRGDASSPAPATTLAQPQQNQTQTHHTTQQTFL |
| .NPYSGDLTKFG..DASSPAPATTLAQPQQNQTQ.HHTTQQTFL | |
| Retrocopy | GNPYSGDLTKFGLWDASSPAPATTLAQPQQNQTQNHHTTQQTFL |
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 |
|---|---|---|
| SRP051959_colon | 0 .33 RPM | 27 .49 RPM |
| SRP051959_heart | 0 .28 RPM | 30 .94 RPM |
| SRP051959_kidney | 0 .31 RPM | 37 .69 RPM |
| SRP051959_liver | 0 .19 RPM | 21 .77 RPM |
| SRP051959_lung | 0 .55 RPM | 38 .31 RPM |
| SRP051959_lymph_node | 0 .34 RPM | 37 .58 RPM |
| SRP051959_skeletal_muscle | 0 .50 RPM | 28 .96 RPM |
| SRP051959_spleen | 0 .29 RPM | 39 .08 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3909 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3909 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3909 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000009677 | 1 retrocopy |
retro_cjac_3909 ,
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