RetrogeneDB ID: | retro_cjac_2970 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:24621620..24623785(-) | ||
| Located in intron of: | ENSCJAG00000004914 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000004996 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KAT2B | ||
| Ensembl ID: | ENSCJAG00000003744 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2970
TGGAAAAACCCCAACCCCTCACCCACTCTCCCCAGAGCCGATCTGCAGCAAATATTTGTCAGTCTAATGAATCCTGTCGG
AGTTGTAGCCATGCCCTAGCTGCTCAGGTTTCCCACCTGGAGAATGTGTCAGAGGAAGAAATGAACAGACTCCTGGGAAT
AGTGTTGGATGTGGAATATCTCTTTACCTGTGTCCACAAGGAAGAAGATGCAGATACCAAGCAAGTTTATTTCTACCTAT
TTAAGCTCTTGAGAAAGTCTATTTTACAAAGAGGAAAACCTGTGGTTGAAGGCTCTTTGGAAAAGAAACCCCCATTTGAA
AAACCTAGCATTGAACAGGGTGTGAATAACTTCGTACAGTACAAATTTAGTCACCTGCCAGCAAAAGAAAGGCAAACAAT
AGTTGAGCTGGCAAAAATGTTCCTAAACCGGATCAACTATTGGCACCTGGAAGCACCATCTCAACGAAGACTGCGATCGC
CCAATGATGTTATTTCTGGATACAGGGAGAATTACACAAGGTGGCTGTGTTACTGCAACGTTCCACAGTTCTGCGACAGT
CTACCTCGGAACGAAACCACACAGGTGTTTGGGAGAACATTGCTTCGCTCGGTCTTCACGGTTATGAGGCGACAGCTCCT
GGAACAAGCAAGACAAGAAAAAGATCAACTGCCTCTTGAAAAACGAACTCTAATCCTCACCCATTTCCCAAAATTTCTGT
CCATGTTAGAAGAAGAAGTTTATAGTCAAAACTCCCCCATCTGGGATCAGGATTTTCTCTCAGCTTCTTCCAGAACCAGC
CAGCTAGGCATCCAAACAGTTATCAGTCCACCTCCTGTGGCTGGGACAACTTCATACAATTCAACCTCATCTTCCCTTGA
GCAGCCAAATGCAGGGAGCAGCAGTCCTGCCTGCAAAGCCTCTTCTGGACTTGAAGCAAACCCAGGAGAAAAGAGGAAAA
TGACTGATTCTCATATTCTGGAGGAGGCCAAGAAACCCCGAGTTATGGGGGATATTGCGATGGAATTAATCAACGAGGTT
ATGTCTACCATCACGGACGCTGCAGCAATGCTCGGACCAGAGACCAATTTTCTGTCAGCACATTCAGCCAGGGATGAGGC
GGCCAGGTTGGAAGAGCGCAGGGGTGTAATTGAATTCCACGTAGTTGGCAACTCCCTCAACCAGAAACCAAACAAGAAGA
TCCTGATGTGGCTGGTCGGACTTCAGAACGTTTTCTCCCACCAGCTGCCCCGAATGCCAAAAGAATACATCACAGGGCTT
GTCTTTGACCCGAAACACAAAACACTTGCTTTAATTAAAGATGGCCGTGTCATTGGTGGTATCTGTTTCCGTATGGTTCC
ATCTCAAGGATTCACAGAGATTGTCTTCTGTGCTGTAACCTCAAATGAGCAAGTCAAGGGCTATGGAACACATCTGATGA
ATCATTTAACAGAATATCACATAAAACATGACATCCTGAACTTCCTCACATATGCAGATGAGTATGCAATTGGATACTTT
AAGAAACAGGGTTTCTTCAAAGAAATTAAAATACCTAAAACCAAATATGTTGGCTATATCAAGGATTATGAAGGAGCCAC
CTTAATGGGGTGTGAGCTAAATCCACGGATTCCATATACAGAATTTTCTGTCATCATTAAAAAGCAGAAGGAGATCATTA
AAAAGCTGATTGAAAGAAAACAGGCACAGATTCGAAAAGTTTACCTTGGACTTTCATGTTTTAAAGATGGAGTTCGACAG
ATTCCTATAGAAAGCATTCCAGGAATTAGAGAGACAGGCTGGAAACCGAGTGGAAAAGAGAAAAGTAAAGAGCCCAAAGA
CCCTGACCAGCTTTATAGCACACTCAAGAGCATCCTCCAGCAGGTGAAGAGCCATCAAAGCGCTTGGCCCTTCATGGAAC
CTGTGAAGAGAACAGAAGCTCCAGGATATTATGAAGTTATAAGGTTCCCCATGGATCTGAAAACCATGAGTGAACGCCTC
AAGAATAGGTACTACGTGTCTAAGAAATTTTTCATGGCAGACTTACAGCGAGTCTTTACCAATTGCAAAGAGTACAACCT
CCCTGCGAGTGAATACTACAAATGTGCCAATATCCTGGAGAAATTCTTCTTCAGTAAAATTAAGGAAGCTGGATTAATTG
ACAAG
ORF - retro_cjac_2970 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.55 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | WKNPNPSPTPPRADLQQIFVSL-TESCRSCSHALEAAHVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKE |
| WKNPNPSPT.PRADLQQIFVSL..ESCRSCSHAL.AA.VSHLENVSEEEMNRLLGIVLDVEYLFTCVHKE | |
| Retrocopy | WKNPNPSPTLPRADLQQIFVSL<NESCRSCSHAL-AAQVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKE |
| Parental | EDADTKQVYFYLFKLLRKSILQRGKPVVEGSLEKKPPFEKPSIEQGVNNFVQYKFSHLPAKERQTIVELA |
| EDADTKQVYFYLFKLLRKSILQRGKPVVEGSLEKKPPFEKPSIEQGVNNFVQYKFSHLPAKERQTIVELA | |
| Retrocopy | EDADTKQVYFYLFKLLRKSILQRGKPVVEGSLEKKPPFEKPSIEQGVNNFVQYKFSHLPAKERQTIVELA |
| Parental | KMFLNR----NLEAPSQRRLRSPNDDISGYKENYTRWLCYCNVPQFCDSLPRYETTQVFGRTLLRSVFTV |
| KMFLNR.....LEAPSQRRLRSPND.ISGY.ENYTRWLCYCNVPQFCDSLPR.ETTQVFGRTLLRSVFTV | |
| Retrocopy | KMFLNRINYWHLEAPSQRRLRSPNDVISGYRENYTRWLCYCNVPQFCDSLPRNETTQVFGRTLLRSVFTV |
| Parental | MRRQLLEQARQEKDKLPLEKRTLILTHFPKFLSMLEEEVYSQNSPIWDQDFLSASSRTSQLGIQTVISPP |
| MRRQLLEQARQEKD.LPLEKRTLILTHFPKFLSMLEEEVYSQNSPIWDQDFLSASSRTSQLGIQTVISPP | |
| Retrocopy | MRRQLLEQARQEKDQLPLEKRTLILTHFPKFLSMLEEEVYSQNSPIWDQDFLSASSRTSQLGIQTVISPP |
| Parental | PVAGTISYNSTSSSLEQPNAGSSSPACKASSGLEANPGEKRKMTDSHILEEAKKPRVMGDIPMELINEVM |
| PVAGT.SYNSTSSSLEQPNAGSSSPACKASSGLEANPGEKRKMTDSHILEEAKKPRVMGDI.MELINEVM | |
| Retrocopy | PVAGTTSYNSTSSSLEQPNAGSSSPACKASSGLEANPGEKRKMTDSHILEEAKKPRVMGDIAMELINEVM |
| Parental | STITDPAAMLGPETNFLSAHSARDEAARLEERRGVIEFHVVGNSLNQKPNKKILMWLVGLQNVFSHQLPR |
| STITD.AAMLGPETNFLSAHSARDEAARLEERRGVIEFHVVGNSLNQKPNKKILMWLVGLQNVFSHQLPR | |
| Retrocopy | STITDAAAMLGPETNFLSAHSARDEAARLEERRGVIEFHVVGNSLNQKPNKKILMWLVGLQNVFSHQLPR |
| Parental | MPKEYITRLVFDPKHKTLALIKDGRVIGGICFRMFPSQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHI |
| MPKEYIT.LVFDPKHKTLALIKDGRVIGGICFRM.PSQGFTEIVFCAVTSNEQVKGYGTHLMNHL.EYHI | |
| Retrocopy | MPKEYITGLVFDPKHKTLALIKDGRVIGGICFRMVPSQGFTEIVFCAVTSNEQVKGYGTHLMNHLTEYHI |
| Parental | KHDILNFLTYADEYAIGYFKKQGFSKEIKIPKTKYVGYIKDYEGATLMGCELNPRIPYTEFSVIIKKQKE |
| KHDILNFLTYADEYAIGYFKKQGF.KEIKIPKTKYVGYIKDYEGATLMGCELNPRIPYTEFSVIIKKQKE | |
| Retrocopy | KHDILNFLTYADEYAIGYFKKQGFFKEIKIPKTKYVGYIKDYEGATLMGCELNPRIPYTEFSVIIKKQKE |
| Parental | IIKKLIERKQAQIRKVYPGLSCFKDGVRQIPIESIPGIRETGWKPSGKEKSKEPKDPDQLYSTLKSILQQ |
| IIKKLIERKQAQIRKVY.GLSCFKDGVRQIPIESIPGIRETGWKPSGKEKSKEPKDPDQLYSTLKSILQQ | |
| Retrocopy | IIKKLIERKQAQIRKVYLGLSCFKDGVRQIPIESIPGIRETGWKPSGKEKSKEPKDPDQLYSTLKSILQQ |
| Parental | VKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESE |
| VKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKK.FMADLQRVFTNCKEYN.P.SE | |
| Retrocopy | VKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKFFMADLQRVFTNCKEYNLPASE |
| Parental | YYKCANILEKFFFSKIKEAGLIDK |
| YYKCANILEKFFFSKIKEAGLIDK | |
| Retrocopy | YYKCANILEKFFFSKIKEAGLIDK |
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 | 1 .06 RPM | 12 .05 RPM |
| SRP051959_heart | 2 .19 RPM | 29 .77 RPM |
| SRP051959_kidney | 1 .44 RPM | 18 .88 RPM |
| SRP051959_liver | 2 .19 RPM | 33 .38 RPM |
| SRP051959_lung | 3 .20 RPM | 42 .47 RPM |
| SRP051959_lymph_node | 2 .40 RPM | 28 .01 RPM |
| SRP051959_skeletal_muscle | 2 .05 RPM | 24 .96 RPM |
| SRP051959_spleen | 2 .48 RPM | 38 .80 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2970 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2970 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2970 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003744 | 1 retrocopy |
retro_cjac_2970 ,
|
| Mus musculus | ENSMUSG00000000708 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000003459 | 1 retrocopy |