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 symbol: DCPS
• Ensembl ID: ENSCJAG00000008896
• Aliases: None
• Description: decapping enzyme, scavenger [Source:HGNC Symbol;Acc:29812]

Sequence

>retro_cjac_1833
ATGGCGGACGCAGCGCCTCAACCCAGCAAGAGAAAGTGCAAGCTGGACATGGAGGAGGCGCACGCTGCCAGCACAGAGGA
AAAGGAGGCAGGTGTTGGAAATGGTACCTGTGCTCCTGTCTGCTTACCATTCTCTGGCTTCAGAGCCCAGAAAGTGCTGA
GGGAGTCTGCATGGGACAAAATCATTTTCCTACAAGGAAAAGTGAATGAGGCCTCTGGAGATGGGGATGGAGAGGATGCC
ATTGTGATCCTGGAGAGGTCAACATTTCAGGTGGGACACGTGGCTCGGCTCCTGACAGGCAGCCCTGAGCTCCAGTTGCA
GTTCTCCAATGATATCTACAGTACCTATCATTTTTTCCCTCCAAGACAACTGAGTGATGTGAAGATGATGTGGTTTACCC
CGCCACAGAGAAACACCTGCAGAAATACCTGCGCCAGGACCTCCACCTGATCTGAGAGACAGGAGATGACTACAGGAACA
TTACTTTACCTCCCCTGGAGTCCCAGAGCCTCAGCATCCAGTGAGTATATAACTTTCTCGACAAGAAGGCTGAAGTGGAC
TGGATTGTTTTTGAGAACCCAGATCCCTCTGACAGGTTTGTCCTCATCCCTGACCTCAAGTGGAACCAACAGCAGCTCGA
TGACCTGTACTTGATCGCCATCTGCCATCGCCGGGGCATCAGATCCCTATGCGACCTTACTCCAGAGCACCTGCTGCTGC
TCAGGAACATCCTTCACCAGGGCAGGAAGCCATCATGCAGCGCTACCAGATGACGGGAGACCATCTGCGAGTATACCTGC
ACTACCTGCCCTCTTACTACCGCCTGCATGTGCACTTCACCACCTTGGGCTTCGAGGCCCCAGCTCAGGTTTGGAGCGAG
CACATCTGCTGGCTGAGGTGATTGAGAACCTGGAGTGTGACCCCAAGTGCTACCAGCAGCACACACTCACCTTCACCCTC
AGGGCTGACGACCCTGCACTCAAGCTCCTGCAGGAGGCTCAGCAAAGC

Alignment

ORF - retro_cjac_1833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 100. %
• 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

Expression

RNA-Seq

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1833 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1833 has 0 orthologous retrocopies within eutheria group .

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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	retro_ocun_97,