RetrogeneDB ID: retro_cjac_4014

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288437.1:1482..2364(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008665
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DARS
• Ensembl ID: ENSCJAG00000011967
• Aliases: None
• Description: None

Sequence

>retro_cjac_4014
CGAGAAACTTTAATTAACAAAGGTTTTGTGGAAATCCAAACTCATAAAATTATTTCAGCTGCCAGTGAAGGAAGAGCCAA
TGTTTTTACTGTGTCATTTTAAAAATAATGCATACCTGGCTCAGTCCCCACAACTGTATAAGCAAATGTGCATTTGTGCT
GATTTTGAGAAGGTTTTCTGTATTGGACCAGTATTCAGAGCAGAAGACTCTAATACCCATAGACATCTAACTGAGTTTGT
TGGTTTGGACATTGAAATGGCTTTTGATTACCATTACCACGAAGTTATGGAAGAAATTGCTGACACCATGTACCAATATT
TAAAGGACTTCAAGAAAGGTTTCAGACTGAAATTCAAATGGTGAATAAACAGTTCCCATGTGAGCCATTCAAATTTTTGG
AGCCAACTCTAAGACGAGAATATTGTGAAGCATTGGCTATGCTTAGGGAAGCTGGAGCCGAAATGGGAGATGAAGATGAT
CTGAGTACACCAAATGAAAAGCTGTTGGGTCATTTGGTAAAGGAAACGTGTGATACGGATTTTTGTGTTCTTGATAAATA
TCCATTGGCTGTAATACCTTTCTACACCATGCCTGACCCGAGAAATCCTAAACAGTCCAACTCTTATGTTATGTTCATAA
GAGGAGAAGAAATATTGGCAGGAGCTCAAAGAATACATGATCCTCAGCTGCCAACAGAGAGAGCTTTCCATCATGGAATT
GATTTGGAGAAAATTAAGGCTTACATTGATTCCTTCTGCTTTGGAGCTCCTCCTCATGCTGGCGGAGGCATTGGGTTGGA
ACGAGTGACTATGCTGTTTCTGGGATTGCATAATGTTCGTCAGACCTCCATGTTCCCTCGTGATCCCAAACGACTCACTC
CT

Alignment

ORF - retro_cjac_4014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.23 %
• Parental protein coverage: 58.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RETLINKGFVEIQTPKIISAASEGGAN-VFTVSYFKNNAYLAQSPQLYKQMCICADFEKVFCIGPVFRAE
          RETLINKGFVEIQT.K.I..A...G....F....FKNNAYLAQSPQLYKQMCICADFEKVFCIGPVFRAE
Retrocopy RETLINKGFVEIQTHK-IISAASEGRA>MFLLCHFKNNAYLAQSPQLYKQMCICADFEKVFCIGPVFRAE

Parental  DSNTHRHLTEFVGLDIEMAFNYHYHEVMEEIADTMVQ-IFKGLQERFQTEIQTVNKQFPCEPFKFLEPTL
          DSNTHRHLTEFVGLDIEMAF.YHYHEVMEEIADTM.Q.IFKGLQERFQTEIQ.VNKQFPCEPFKFLEPTL
Retrocopy DSNTHRHLTEFVGLDIEMAFDYHYHEVMEEIADTMYQ<IFKGLQERFQTEIQMVNKQFPCEPFKFLEPTL

Parental  RLEYCEALAMLREAGVEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRPFYTMPDPRNPKQSN
          R.EYCEALAMLREAG.EMGDEDDLSTPNEKLLGHLVKE..DTDF..LDKYPLAV.PFYTMPDPRNPKQSN
Retrocopy RREYCEALAMLREAGAEMGDEDDLSTPNEKLLGHLVKETCDTDFCVLDKYPLAVIPFYTMPDPRNPKQSN

Parental  SYDMFMRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFRFGAPPHAGGGIGLERVTMLFLGLH
          SY.MF.RGEEIL.GAQRIHDPQL.TERA.HHGIDLEKIKAYIDSF.FGAPPHAGGGIGLERVTMLFLGLH
Retrocopy SYVMFIRGEEILAGAQRIHDPQLPTERAFHHGIDLEKIKAYIDSFCFGAPPHAGGGIGLERVTMLFLGLH

Parental  NVRQTSMFPRDPKRLTP
          NVRQTSMFPRDPKRLTP
Retrocopy NVRQTSMFPRDPKRLTP

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	0.00 RPM	23.39 RPM
SRP051959_heart	0.00 RPM	31.50 RPM
SRP051959_kidney	0.00 RPM	31.39 RPM
SRP051959_liver	0.02 RPM	28.18 RPM
SRP051959_lung	0.02 RPM	23.38 RPM
SRP051959_lymph_node	0.00 RPM	25.80 RPM
SRP051959_skeletal_muscle	0.04 RPM	49.24 RPM
SRP051959_spleen	0.00 RPM	28.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4014 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4014 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011967	1 retrocopy	retro_cjac_4014 ,