RetrogeneDB ID: | retro_cjac_562 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:81479848..81481378(-) | ||
| Located in intron of: | ENSCJAG00000004536 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000004586 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SH3KBP1 | ||
| Ensembl ID: | ENSCJAG00000005449 | ||
| Aliases: | None | ||
| Description: | SH3-domain kinase binding protein 1 [Source:HGNC Symbol;Acc:13867] |
Retrocopy-Parental alignment summary:
>retro_cjac_562
GTGGAGGCCATAGTGGAGTTTGACTACCAGGCCCAGCACGACGATGAGCTGACAATCAGCTTGGATGGCATCATCACCAA
CATCAGGAAGGAGGATGGAGGCTGGTGGGAGGGACAGATCAACGGCTGGAGAGGTTTGTTGTCTGACAACTTTGTAAGAG
AAATAAAGAAAGAGATGAAGAAAGACCCTCTCGCCAATAAAGCTCCAGAAAAGCCCATGCATGAAGTGCCCAGTGGAAAC
TCTTTGCTGTCTTCTGAGACGATTTTAAAAGAACCAATAAGAGAGGCGAGCGACTGAGGCGCCAGTGTCAGGTAGCATTC
AGCTACCTGCCCCAGAATGATGATGAACTTGAGCTGAAAATTGGCGACATCGAAGAGGTGGTAGGAGAGGTAGAGGAAGG
ATGGTGGGAAGGTGTTCTCAACGGGAAGACTGGAATGTTTCCTTCCAACTTCATCAAGGAGTTGTCAGGGGAGTCGGATG
AGCTTGGCATTTCCCAGGATGAGCAGCTGTCCAAGTCAAGTTTAAGGGAAACCACAGGCTCCGAGAGTGATGGGGGTGAC
TCAAGCAGCACCAGGTCTGAAGGTGCCAATGGGACAGTGGCAACTGCAGCAATCCAGCCCAAGAAAGTTAAAGGAGTGGG
CTTTGGAGACATTTCAAAGACAAGCCAATCAAACTAAGACCAAGATCAATTGAAGTAGAAAATGACTTTCTGCCGGTGGA
AAAGACTATTGGGAAGAAGCTACCTGCAACTAAGCAACTCCAGACTCATCAAAAACAGAAATGGACAGCAGGACAAAGAG
CAAGGATTACTGCAAAGTAATATTTCCATATGAGGCACAGAATGATGAATTGACAATCAAAGAAGGAGATATAGTCATTC
TCATCAATAGGGACTGCATTGACATAGGGTGGTGGGAAGGAGAGCTGAACGGCAGACGAGGCATGTTCCCTGATAACTTT
GTGAAGTTACTTCCACCGGACTTTGAAAAGGAGGGGAATAGACCCAAGAAGCCACCACCTCCATCCGCTCCTGTCATCAA
ACAAGGGGCAGGTACCACTGAGAGAAAACATGAACTTAAAAAGATACCTCCTGAAAGACCAGAAATGCTTCCCAACAGAA
CAGAAGAAAAAGAAAGACCAGAGAGAGAGAGAGAGCCAAAACTGGATTTACAGAAGTCCTCCGTTCCTGACATACCGTCA
AAAAAGCCTTGGCCACCTAAGACCAATTCTCTCAGCAGACCTGGTGCACTGCCCCCAAGAAGGCCAGAGCGACCGGTGGG
TCCACTGACACACACCAGGGGTGACCGTCCAAAGATTGACTTGGTGGGCAGTTCGCTTTCTGGCATCCTGGACAAAGATC
TCTCGGACCTCAGCAATGACATCGACCTAGAAGGTTTTGACTCCGTGATGTCATCTACTGAGAAACTCAGTCATCCGACC
ACAAGAAGACCAAAAGCTATGGGGAGGCGGCCTCCATCCCAGTCCCTCACATCTGTGTCGGACAACAAAGCATCCCTGCC
ACCCACTCCG
ORF - retro_cjac_562 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.29 % |
| Parental protein coverage: | 93.74 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKKEMKKDPLANKAPE |
| VEAIVEFDYQAQHDDELTIS...IITNIRKEDGGWWEGQING.RGL..DNFVREIKKEMKKDPLANKAPE | |
| Retrocopy | VEAIVEFDYQAQHDDELTISLDGIITNIRKEDGGWWEGQINGWRGLLSDNFVREIKKEMKKDPLANKAPE |
| Parental | KPMHEVPSGNSLLSSETIL-RTNKRGERRRRR-CQVAFSYLPQNDDELELKVGDIIEVVGEVEEGWWEGV |
| KPMHEVPSGNSLLSSETIL.........R.RR.CQVAFSYLPQNDDELELK.GDI.EVVGEVEEGWWEGV | |
| Retrocopy | KPMHEVPSGNSLLSSETIL<KRTNKRGERLRRQCQVAFSYLPQNDDELELKIGDIEEVVGEVEEGWWEGV |
| Parental | LNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSSTKSEGANGTVATAAIQPKK |
| LNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSST.SEGANGTVATAAIQPKK | |
| Retrocopy | LNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSSTRSEGANGTVATAAIQPKK |
| Parental | VKGVGFGDI-FKDKPIKLRPRSIEVENDFLPVEKTIGKKLPATT-ATPDSSKTEMDSRTKSKDYCKVIFP |
| VKGVGFGDI.FKDKPIKLRPRSIEVENDFLPVEKTIGKKLPAT..ATPDSSKTEMDSRTKSKDYCKVIFP | |
| Retrocopy | VKGVGFGDI<FKDKPIKLRPRSIEVENDFLPVEKTIGKKLPATK<ATPDSSKTEMDSRTKSKDYCKVIFP |
| Parental | YEAQNDDELTIKEGDIVTLINKDCIDVGWWEGELNGRRGVFPDNFVKLLPPDFEKEGNRPKKPPPPSAPV |
| YEAQN.DELTIKEGDIV.LIN.DCID.GWWEGELNGRRG.FPDNFVKLLPPDFEKEGNRPKKPPPPSAPV | |
| Retrocopy | YEAQN-DELTIKEGDIVILINRDCIDIGWWEGELNGRRGMFPDNFVKLLPPDFEKEGNRPKKPPPPSAPV |
| Parental | IKQGAGTTERKHELKKIPPERPEMLPNRTEEKERP--EREPKLDLQKPSVPAIPPKKPRPPKTNSLSRPG |
| IKQGAGTTERKHELKKIPPERPEMLPNRTEEKERP..EREPKLDLQK.SVP.IP.KKP.PPKTNSLSRPG | |
| Retrocopy | IKQGAGTTERKHELKKIPPERPEMLPNRTEEKERPEREREPKLDLQKSSVPDIPSKKPWPPKTNSLSRPG |
| Parental | ALPPRRPERPVGPLTHTRGDGPKIDLAGSSLSGILDKDLSDRSNDIDLEGFDSVVSSTEKLSHPTTSRPK |
| ALPPRRPERPVGPLTHTRGD.PKIDL.GSSLSGILDKDLSD.SNDIDLEGFDSV.SSTEKLSHPTT.RPK | |
| Retrocopy | ALPPRRPERPVGPLTHTRGDRPKIDLVGSSLSGILDKDLSDLSNDIDLEGFDSVMSSTEKLSHPTTRRPK |
| Parental | ATGRRPPSQSLTSSSLSSPDIFDSP |
| A.GRRPPSQSLTS.S.........P | |
| Retrocopy | AMGRRPPSQSLTSVSDNKASLPPTP |
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 .11 RPM | 4 .90 RPM |
| SRP051959_heart | 0 .51 RPM | 6 .75 RPM |
| SRP051959_kidney | 0 .20 RPM | 7 .01 RPM |
| SRP051959_liver | 0 .06 RPM | 2 .58 RPM |
| SRP051959_lung | 0 .91 RPM | 15 .86 RPM |
| SRP051959_lymph_node | 0 .89 RPM | 23 .63 RPM |
| SRP051959_skeletal_muscle | 0 .11 RPM | 2 .47 RPM |
| SRP051959_spleen | 0 .42 RPM | 15 .65 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_562 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_562 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_562 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005449 | 2 retrocopies |
retro_cjac_3599, retro_cjac_562 ,
|