RetrogeneDB ID: retro_cjac_2409

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:13697753..13698952(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021566
• Aliases: None
• Description: None

Sequence

>retro_cjac_2409
CTGCAGCGGAAGATGGAGAACCGTGATTACCGGGATGCACAGGAGTTTCCTGCTGACGTACGGCTTATGTTCTCTAACTG
CTATAAGTACAACCCCCCAGATCACGATGTTGTGGCAATGGCACAAAAGCTACAGGACATATTTGACTTCCGTTATGCCA
AGATGCCAGATGAACCACTGGAACCAGGGCCTTTACCAGTCTCTACTGCCACATGCCCCCTGGCTGGCCCAAATTATCTT
CAGAGTCCTCCAGTGAGGAAAGTAGCAGTGAGAGCTCCTCTGAGGAAGAGGAGGAGGAAGATGAGGAGGACGAGGAACAA
GAAGAGAGTGAAAGCTCAGACCCAGACGAAGAAAGGGCTCATCGCTTGACAGTACACAGGGACAGCTTCGGGCAGTACAT
GAACAACTGGCTGCTCTGTCCCAGGGTCCAATATCCAAGCCCAAGAGGAAAAGAGAGAAAAAGAAGAAACAGAAGGCAGA
GAAGCACGGAGGACGAGCTGGGGTTGATGAAGATGACAAGGGGCCTTGAGCACCCCTGCCCACCTCAGCCCAAGAAGTCC
AGGAAAGCAAGTGGCAATGGAGGTGGCAGTGCTGCTTTAGGCCCTTCTGGCTTTGGACCTTCTGGAGGAAGTGGCACCAA
GCTCCCCAAAAAGGCCACAAAGACAGCCCCACCTGCCCTGCCAACAGGTCATGATTCAGAGGAGGAGGAAGAGAGCAGGC
CCAAGAGTTAGGATGAAAAGCGGCAGCTGGGCCTGGACATTAACAAATAACCTGGAGAGAAGCTGGGCCAACTTGTGCAC
ATAATCCAAGCCAGGGAACCCTCTTTACATGATTCAAACCCAGAAGAGATTGAGATTGATTTTGAAACACTCAAGCCATC
CACACTCAGAGAGCTTGAGCGCTATGTCCTTTCCTGCCTATGTAAGAAACCTCACAAGCCCTACACCATTAAGGAGGCTG
TGGGAAAGACAAAGGAAGAACTGGCTTTGGAGAAAAAGTGGGAATTAGAAAAGCAGTTACAAGATGTCAGCGGACAGCTC
AATTCCACTAAAAAGCCCCCCAAGAAAGCGAGTGAGAAAACAGAGTCATCCTCTGCACAGCAAGTAATAGTGTCACACCT
TAGTGCTTCCAGCTCCAGCTCAGATTCCAGCTCCTCCTCTTCGTCATCTTTTTCAGACACCAGTGATTCAGACTCAGGC

Alignment

ORF - retro_cjac_2409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.84 %
• Parental protein coverage: 59.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTA
          ..RKMENRDYRDAQEF.ADVRLMFSNCYKYNPPDHDVVAMA.KLQD.F.FRYAKMPDEPLEPGPLPVSTA
Retrocopy LQRKMENRDYRDAQEFPADVRLMFSNCYKYNPPDHDVVAMAQKLQDIFDFRYAKMPDEPLEPGPLPVSTA

Parental  IPPGLAKSSSES-SSEE-SSSESSSEEEEEEDEEDEE-EESESSDSEEERAHRLA-ELQEQLRAVHEQLA
          ..P........S.SS.E.SSSESSS..........EE.EESESSD..EERAHRL....Q.QLRAVHEQLA
Retrocopy TCPLAGPNYLQS<SSSEESSSESSSXXXXXXXXXXEEQEESESSDPDEERAHRLT<STQGQLRAVHEQLA

Parental  ALSQGPISKPKRKREKKEKKKKRKAEKHRGRAGADEDDKGPRAPR-PPQPKKSKKASVSGGGSAALGPSG
          ALSQGPISKPKRKREKK...KK.KAEKH.GRAG.DEDDKGP.AP..PPQPKKS.KAS..GGGSA......
Retrocopy ALSQGPISKPKRKREKK---KKQKAEKHGGRAGVDEDDKGP*APL>PPQPKKSRKASGNGGGSAXXXXXX

Parental  FGPSGGSGTKLPKKATKTAPPALPTGYDSEEEEESRPMSYDEKRQLSLDINKLPGEKLGRVVHIIQAREP
          .....GSGTKLPKKATKTAPPALPTG.DSEEEEESRP.S.DEKRQL.LDINK.PGEKLG..VHIIQAREP
Retrocopy XXXXXGSGTKLPKKATKTAPPALPTGHDSEEEEESRPKS*DEKRQLGLDINK*PGEKLGQLVHIIQAREP

Parental  SLRDSNPEEIEIDFETLKPSTLRELERYVLSCLRKKPRKPYTIKKPVGKTKEELALEKKRELEKRLQDVS
          SL.DSNPEEIEIDFETLKPSTLRELERYVLSCL.KKP.KPYTIK..VGKTKEELALEKK.ELEK.LQDVS
Retrocopy SLHDSNPEEIEIDFETLKPSTLRELERYVLSCLCKKPHKPYTIKEAVGKTKEELALEKKWELEKQLQDVS

Parental  GQLNSTKKPPKKASEKTESSSAQQVVVSRLSASSSSSDSSSSSSSSSSSDTSDSDSG
          GQLNSTKKPPKKASEKTESSSAQQV.VS.LSASSSSSD.SSSSSSSS.SDTSDSDSG
Retrocopy GQLNSTKKPPKKASEKTESSSAQQVIVSHLSASSSSSD-SSSSSSSSFSDTSDSDSG

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	53.38 RPM
SRP051959_heart	0.00 RPM	53.22 RPM
SRP051959_kidney	0.02 RPM	73.99 RPM
SRP051959_liver	0.00 RPM	46.18 RPM
SRP051959_lung	0.00 RPM	81.14 RPM
SRP051959_lymph_node	0.02 RPM	77.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	37.74 RPM
SRP051959_spleen	0.00 RPM	74.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2409 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021566	2 retrocopies	retro_cjac_2409 , retro_cjac_564,
Oryctolagus cuniculus	ENSOCUG00000003097	1 retrocopy	retro_ocun_710,