RetrogeneDB ID: | retro_cjac_1833 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:114167340..114168348(+) | ||
| Located in intron of: | ENSCJAG00000010444 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DCPS | ||
| Ensembl ID: | ENSCJAG00000008896 | ||
| Aliases: | None | ||
| Description: | decapping enzyme, scavenger [Source:HGNC Symbol;Acc:29812] |
Retrocopy-Parental alignment summary:
>retro_cjac_1833
ATGGCGGACGCAGCGCCTCAACCCAGCAAGAGAAAGTGCAAGCTGGACATGGAGGAGGCGCACGCTGCCAGCACAGAGGA
AAAGGAGGCAGGTGTTGGAAATGGTACCTGTGCTCCTGTCTGCTTACCATTCTCTGGCTTCAGAGCCCAGAAAGTGCTGA
GGGAGTCTGCATGGGACAAAATCATTTTCCTACAAGGAAAAGTGAATGAGGCCTCTGGAGATGGGGATGGAGAGGATGCC
ATTGTGATCCTGGAGAGGTCAACATTTCAGGTGGGACACGTGGCTCGGCTCCTGACAGGCAGCCCTGAGCTCCAGTTGCA
GTTCTCCAATGATATCTACAGTACCTATCATTTTTTCCCTCCAAGACAACTGAGTGATGTGAAGATGATGTGGTTTACCC
CGCCACAGAGAAACACCTGCAGAAATACCTGCGCCAGGACCTCCACCTGATCTGAGAGACAGGAGATGACTACAGGAACA
TTACTTTACCTCCCCTGGAGTCCCAGAGCCTCAGCATCCAGTGAGTATATAACTTTCTCGACAAGAAGGCTGAAGTGGAC
TGGATTGTTTTTGAGAACCCAGATCCCTCTGACAGGTTTGTCCTCATCCCTGACCTCAAGTGGAACCAACAGCAGCTCGA
TGACCTGTACTTGATCGCCATCTGCCATCGCCGGGGCATCAGATCCCTATGCGACCTTACTCCAGAGCACCTGCTGCTGC
TCAGGAACATCCTTCACCAGGGCAGGAAGCCATCATGCAGCGCTACCAGATGACGGGAGACCATCTGCGAGTATACCTGC
ACTACCTGCCCTCTTACTACCGCCTGCATGTGCACTTCACCACCTTGGGCTTCGAGGCCCCAGCTCAGGTTTGGAGCGAG
CACATCTGCTGGCTGAGGTGATTGAGAACCTGGAGTGTGACCCCAAGTGCTACCAGCAGCACACACTCACCTTCACCCTC
AGGGCTGACGACCCTGCACTCAAGCTCCTGCAGGAGGCTCAGCAAAGC
ORF - retro_cjac_1833 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.59 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MADAEPQPSKRKRELDLEEAHAASTEEKKADVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNE |
| MADA.PQPSKRK..LD.EEAHAASTEEK.A.VGNGTCAPV.LPFSGFR.QKVLRESA.DKIIFL.GKVNE | |
| Retrocopy | MADAAPQPSKRKCKLDMEEAHAASTEEKEAGVGNGTCAPVCLPFSGFRAQKVLRESAWDKIIFLQGKVNE |
| Parental | ASGDGAGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLSDVK-TTVVYPATQKH |
| ASGDG.GEDA.VILE...FQV..VA.LLTGSPELQLQFSNDIYSTYH.FPPRQLSDVK...VVYPAT.KH | |
| Retrocopy | ASGDGDGEDAIVILERSTFQVGHVARLLTGSPELQLQFSNDIYSTYHFFPPRQLSDVK<DDVVYPATEKH |
| Parental | LQKYLRQDLRLIRETGDNYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWN |
| LQKYLRQDL.LI.ETGD.YRNITLP.LESQSLSIQ.VYN.LDKKAE.D.IVFENPDPSD.FVLIPDLKWN | |
| Retrocopy | LQKYLRQDLHLI*ETGDDYRNITLPPLESQSLSIQ*VYNFLDKKAEVDWIVFENPDPSDRFVLIPDLKWN |
| Parental | QQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQ-GQEVILQRYQMTGDRLRVYLHYLPSYYHLHV |
| QQQLDDLYLIAICHRRGIRSL.DLTPEHL.LLRNILHQ.GQE.I.QRYQMTGD.LRVYLHYLPSYY.LHV | |
| Retrocopy | QQQLDDLYLIAICHRRGIRSLCDLTPEHLLLLRNILHQ<GQEAIMQRYQMTGDHLRVYLHYLPSYYRLHV |
| Parental | HFTALGFEA-PGSGVERAHLLAEVIENLECDPKHYQQRTLTFALRADDPLLKLLQEVRQS |
| HFT.LGFEA.P.SG.ERAHLLAEVIENLECDPK.YQQ.TLTF.LRADDP.LKLLQE..QS | |
| Retrocopy | HFTTLGFEA<PSSGLERAHLLAEVIENLECDPKCYQQHTLTFTLRADDPALKLLQEAQQS |
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 .40 RPM | 2 .77 RPM |
| SRP051959_heart | 0 .54 RPM | 2 .63 RPM |
| SRP051959_kidney | 0 .42 RPM | 2 .86 RPM |
| SRP051959_liver | 0 .52 RPM | 1 .52 RPM |
| SRP051959_lung | 0 .72 RPM | 4 .52 RPM |
| SRP051959_lymph_node | 0 .62 RPM | 6 .94 RPM |
| SRP051959_skeletal_muscle | 0 .35 RPM | 2 .05 RPM |
| SRP051959_spleen | 0 .99 RPM | 4 .43 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1833 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1833 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1833 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 | ENSCJAG00000008896 | 1 retrocopy |
retro_cjac_1833 ,
|
| Oryctolagus cuniculus | ENSOCUG00000012520 | 1 retrocopy |