RetrogeneDB ID: retro_cjac_1134

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38420933..38421871(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF362
• Ensembl ID: ENSCJAG00000001133
• Aliases: None
• Description: None

Sequence

>retro_cjac_1134
GACGTTGCGTTGCACGCACGGCTGGCCACCAGCACTGTCACAGGTCTGGGGCTGTCCACCCGGACCCCGGCTGTGAGCAC
TTCTGAGTTGAGCGCAGGCTCTGGCACAGGTACCAGCACCCCGTCCACACCCACCACCACCAGCCAGAGCTGCCTCATCG
CCTCATCCCCCACCCTCATCTCAGGGATCACCAGCCCCTGTCTCCTGGACTCCATCAAGACAACCCAGGGCCATGACCTG
CTTGGCCCCCCCAAGTCCGAATGCGGCCACAAAAAGATCAAGGCAGAGAACCCGGGGGGTCCGCCTGTCTTAGTAGTCCC
CTACCCCATCCTGGTCTCGGGCAAGACTGCCAAGGAGGGCAAGACGTAAGGTATGCCCGCCGACCTTTTTCACCAAGTCG
GAGATGCAGATCACTCCAAGTCGCACACAGAGGCCAAGCCCCACAAGTGCCCGCACTGCTCTAAGTCCTTTGCCAGTGCC
TCCTACCTGGCCCAGCACCTGCGTATCCACCTGGGTGTCAAGCTCTACCACTGCTCCTACTGTGATAAGTCCTTCCGGCA
GCTCTCCCACCTCCAGCAGCACACCAGAATCCACACAGGTGACAGACCCTGCAAGTGCCCACACCCTGGCTGTGAGAAGG
CTTTCACTCAGCTCTCCAACCTGCAGTCTCACCAGCACCAGCACAACAAGGACAAGCCCTACATGTGTCCCAACTGCTAC
TGGGCCTACTCGGACTCCGCCTCCCTGCAGATCCACCTCTCGGCCCACGCCATCAAGCATGCCAAGGCCTACTGCTGCAG
CACGTGTGGGCAGGCCAAACCTCGGAGACCTACCTGATGAAGCACATGTCCAAACACATGGTGGTGGAGCACCTGGTGAG
CCATCACTCACCCCAGAGGATTGAGTCTCCTGGCATCCCGGTGCGAATCTCTCTCATC

Alignment

ORF - retro_cjac_1134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 77.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DVALHARPATSTVTGLGLSTRTPAVSTSESSAGTGTGTSTPSTPTTTSQSRLIASSPTLISGITSPPLLD
          DVALHAR.ATSTVTGLGLSTRTPAVSTSE.SAG.GTGTSTPSTPTTTSQS.LIASSPTLISGITSP.LLD
Retrocopy DVALHARLATSTVTGLGLSTRTPAVSTSELSAGSGTGTSTPSTPTTTSQSCLIASSPTLISGITSPCLLD

Parental  SIKTIQGHGLLGPPKSERGRKKIKAENPGGPPVLVV-PYPILASGETAKEGKTYRCKVCPLTFFTKSEMQ
          SIKT.QGH.LLGPPKSE.G.KKIKAENPGGPPVLVV.P.P...S...A......R.KVCP.TFFTKSEMQ
Retrocopy SIKTTQGHDLLGPPKSECGHKKIKAENPGGPPVLVV>PTP---SWSRARLPRRARRKVCPPTFFTKSEMQ

Parental  I-HSKSHTEAKPHKCPHCSKSFANASYLAQHLRIHLGVKPYHCSYCDKSFRQLSHLQQHTRIHTGDRPYK
          I.HSKSHTEAKPHKCPHCSKSFA.ASYLAQHLRIHLGVK.YHCSYCDKSFRQLSHLQQHTRIHTGDRP.K
Retrocopy I<HSKSHTEAKPHKCPHCSKSFASASYLAQHLRIHLGVKLYHCSYCDKSFRQLSHLQQHTRIHTGDRPCK

Parental  CPHPGCEKAFTQLSNLQSHQRQHNKDKPYKCPNCYRAYSDSASLQIHLSAHAIKHAKAYCCSMCGRA-YT
          CPHPGCEKAFTQLSNLQSHQ.QHNKDKPY.CPNCY.AYSDSASLQIHLSAHAIKHAKAYCCS.CG.A..T
Retrocopy CPHPGCEKAFTQLSNLQSHQHQHNKDKPYMCPNCYWAYSDSASLQIHLSAHAIKHAKAYCCSTCGQA<QT

Parental  SETYLMKHMSKHTVVEHLVSHHSPQRTESPGIPVRISLI
          SETYLMKHMSKH.VVEHLVSHHSPQR.ESPGIPVRISLI
Retrocopy SETYLMKHMSKHMVVEHLVSHHSPQRIESPGIPVRISLI

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	1.55 RPM
SRP051959_heart	0.00 RPM	8.31 RPM
SRP051959_kidney	0.04 RPM	6.39 RPM
SRP051959_liver	0.00 RPM	1.71 RPM
SRP051959_lung	0.00 RPM	4.75 RPM
SRP051959_lymph_node	0.00 RPM	3.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.25 RPM
SRP051959_spleen	0.00 RPM	3.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1134 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1134 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001133	2 retrocopies	retro_cjac_1134 , retro_cjac_544,