RetrogeneDB ID: | retro_cjac_1925 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:74589874..74591022(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000014390 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SUGP1 | ||
| Ensembl ID: | ENSCJAG00000005755 | ||
| Aliases: | SUGP1, SF4 | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1925
AAGGCCTATGGGTGGTTTGGAGTTTCTCCCCCTAAATCTGGAAAAATGAACATGAACATCCTTCACCAAGAAGAGCTCAA
TGCTCAGAAGAAAGGGGAAATTGAAGCCAAAATGGAACAGAAAGCCAAGCAGAATCAGGGGCCAGCCCTCAGTCCCCACA
TCCCAGAGAAATCTCAAATGCACACAACTCTTCCTGCCTTTCCAACAAGTTCGCTAACGACAGTCATTTACTGCAGCAGT
TTTTGAAGTTGCAGAAGGCACAGACCAGCACAGATGCCGGCCCCCACCCCCTACCCAGTGCGCCCACTGCCCCTTCCAGC
ACACTTACCCCCAGTGCAGGAAAGGGGTCCCTCCTCATCAGCAAGCATACAGGCCTGGGGCTGGCCAGCTCCCCGGGCCA
GGTGACGAGCTCTCGCAGTCAAGCAGCTGCTGGTGGCGCACTGTCTGAGTGTCTTCCAGTACCCGGAAGAGAAGGAGGAG
GACTATGAGCAGTGGCTGAAAATCAAACTTTCACTCCCAGAAGGAATCGAGACTCGGAAAATGATAGAGAAATTGGCCCA
CTTTGTGGCAGAGGAGTTAGAAAAAGAAGCTATGGAGGATTACAAGGATAACCCTGCGTTTGCATTTTTGCCTGATAAAG
AATAGCAGGGAATTCCTCTACTACAGAAAGAAGGTGGCTGAGGTAAGAAAGGAAGCGCAGAAGTCCCCGGCAGCCTCTCA
GAAAGTTTCACCCCCAGAGGACGTAGAGGTCAAGAACCTTGCAGAGAACTTGGCCAGGTTCATAGCAGGCAGGGATCCCG
AGTGGAAACCATCACCCTCCAGAACCATCATGAAAATCAGGCATTCAGCTTTCTGTACAAGCCCAACAGCCAAGGGTACA
AGTGCTACTGACAGAAGCTGGAGGAGTTCCAGAAAGCCAAGGCCGGCTCCCCAGGCAACCTCATGGCACAGGACACGGCC
TGAAGCGCAAGTCCTCTCCTGAGGCCTGACCCCAGCCACCACCTGCCCCGCCTCCTCCTCGCCTGTGCCGCCCCCACCCC
CCTACACCCCCACACACACCCCCACCCCCGCTCGTCATACCTGCTCCAGCCACCCCCGGGAAGCCAGACTCCCTCTGCAA
CCACTGTGAAGAGAAAGCAGAAGAGCCG
ORF - retro_cjac_1925 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.59 % |
| Parental protein coverage: | 60.63 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | KANRWFGVAPPKSGKMNMNILHQEELIAQKKREIEAKMEQKAKQNQV-ASPQPPHPGEITNAHNSSCVSN |
| KA..WFGV.PPKSGKMNMNILHQEEL.AQKK.EIEAKMEQKAKQNQ..ASPQ.PHP.EI.NAHNSSC.SN | |
| Retrocopy | KAYGWFGVSPPKSGKMNMNILHQEELNAQKKGEIEAKMEQKAKQNQG<ASPQSPHPREISNAHNSSCLSN |
| Parental | KFANDGSFLQQFL---KLQKSQTSTDTPA-STPIVPPSTPTPSAGKRSLLISRRTGLGLAS-LPGPVKSY |
| KFAND...LQQFL...K.Q.S......P..S.P..P.ST.TPSAGK.SLLIS..TGLGLAS.LPGP.... | |
| Retrocopy | KFANDSHLLQQFLKLQKAQTSTDAGPHPLPSAPTAPSSTLTPSAGKGSLLISKHTGLGLAS<LPGPGDEL |
| Parental | SHA-KQLPVAHRPSVFQSPDEDEEEDYEQWLEIKVSPPEGAETRKVIEKLARFVAEGGPELEKVAMEDYK |
| S...KQL.VAH..SVFQ.P.E..EEDYEQWL.IK.S.PEG.ETRK.IEKLA.FVAE...ELEK.AMEDYK | |
| Retrocopy | SQS<KQLLVAHCLSVFQYPEE-KEEDYEQWLKIKLSLPEGIETRKMIEKLAHFVAE---ELEKEAMEDYK |
| Parental | DNPAFAFLHD-KNSREFLYYRKKVAEIRKEAQKSQAASQKVSPPEDEEVKNLAEKLARFIADGGPE-VET |
| DNPAFAFL.D.KNSREFLYYRKKVAE.RKEAQKS.AASQKVSPPED.EVKNLAE.LARFIA...PE.VET | |
| Retrocopy | DNPAFAFLPD>KNSREFLYYRKKVAEVRKEAQKSPAASQKVSPPEDVEVKNLAENLARFIAGRDPE<VET |
| Parental | IALQNNRENQAFSFLYEPNSQGYKYYRQKLEEFRKTKAGSTGTLTALDPS-LKRKSPPEALSGSLPPATT |
| I.LQN..ENQAFSFLY.PNSQGYK.Y.QKLEEF.K.KAGS.G.L.A.D...LKRKS.PEA.....P.A.. | |
| Retrocopy | ITLQNHHENQAFSFLYKPNSQGYKCY*QKLEEFQKAKAGSPGNLMAQDTA<LKRKSSPEA*PQPPP-APP |
| Parental | CPASSTPAPTITPAPAVSGKPASAATVKRKRKSRWGPEEDKVELP |
| .P....P.P...P..........A.....K..S.....E.K.E.P | |
| Retrocopy | PPRLCRPHPPTPPHTPPPPLVIPAPATPGKPDSLCNHCEEKAEEP |
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 .00 RPM | 7 .14 RPM |
| SRP051959_heart | 0 .00 RPM | 9 .72 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .99 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .20 RPM |
| SRP051959_lung | 0 .00 RPM | 9 .60 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 11 .99 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 12 .45 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1925 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1925 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1925 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005755 | 1 retrocopy |
retro_cjac_1925 ,
|
| Macaca mulatta | ENSMMUG00000028834 | 1 retrocopy |