RetrogeneDB ID: retro_cjac_418

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:75632457..75634016(+)
• Located in intron of: ENSCJAG00000013220

Retrocopy information

• Ensembl ID: ENSCJAG00000013234
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRIM8
• Ensembl ID: ENSCJAG00000018057
• Aliases: None
• Description: None

Sequence

>retro_cjac_418
AACAACTTCTGCCGGGGCTGCATCGGCGAGGCGTGGGCCAAGGACAGCGGCCTTGTGCGCTTTCCAGAGTGCAACCAGGC
CTACAACCAGAAGCCGGGCCTGGAGAAGAACCTGAAGCTCACCAACATCCTGGAGAAGTTCAACGCCCTGCACGTGGAGA
AGCCGCCGCCGGCGCTGCACTGCGTGTTCTGCCGCCGCTGTCCCCCGCTGCCCGCGCAGAAGGTCTGCCTGTGCTGCGAG
GTGCCCTGCTGCCAGTCCCACGTGCAGATGCACCTGCAGCAGCCCTCCACCGCCCGCGGGCACCTCCTGGTGGAGGCGGA
CGACGTGCGGGGCTGGAACTGCCCGCAGCACAACGCCTATCGCCTCTACCACCTCGAGGCCGAGCAGGTGGCAGTTTGCC
AGTACTGCTGCTACTACAGTGGCGCGCATCAGGGACACTCGGTGAGCGACGTGGAGATCCGAAGGAATAAAATCCGGAAG
ATGCTCATGAAGCAGCAGGACCGGCTGGAGGAGCGAGAGCAGGACATTGAGGATCAGCTGTACAAACTCGAGTCAGACAA
GCTACTGGTGGAGGAGAAAGTGAACCAACTGAAGGAGGAAGTTCGACTGCAGTACGAGAAGCTGCACCAGCTGCTAGATG
AGGACCTGCGGCAGACAGTGGAGGTCCTGGACAAGGCCCGGCCAAGTTCTGCAGCGAGAACGCAGCGCAGGCGCTGCACC
TCGGGAAGCACATGCAGGAGGCCAAGAAGCTGCTGGGTTCCCTGCAGCTGCTGTTTGATAAGACGGAGGATGTCAGCTTC
ATGAAGAACCCCAAGTCTGTGAAAATCCTGATGGACAGGACCCAGACCTGCACAGGCAGCAGCCTTTCTCCACCTAAGAT
CGGCCACCTGAACTCCAAGCTCTTTCTGAACCAGGTGGCCAAGAAGGAGAAGCAGCTGCGGAAGATGCTAGAAGGCCCCT
TCAGCACGCTGGTGCCCTTCCTGCAGAGCGTCCCCCTGTACTCTTGCGGCGTCAGCAGCTCTGGGGCAGAAAAGCGCAAG
CACTCAACGGCCTTCCCAGAGGCCAGTTTCCTAGAGATGTTGTCGGGCCCTGTGGGCGGCCAGTACAGGGCGGCGGGCAC
AGCCAGCGGTGAGGGCCAGTCTGGGCAGCCCCTGGGGCCCTGCAGCTCCACACAGCACTTGGTGGCCTTGCCGGGCGGTG
CCCAACCAGTGCACTCAAGCCCCGTGTTCCTCTCATCGCAGTATCCCAATGGCTCTGCCGCCCAGCAGCCCATGCTCCCC
CAGTATGGTGGCCGCAAGACTCTCGTCTGTTCTGTGGACAACTGTTACTGTTTTTCCGTGGCCAACCATGGCGGCCACCA
GCCCTACCCCCGCTCCGGCCACTTTCTCTGGACAGTGCCCTCGCAGGAGTACTCACACCCGCTCCCGCCCACACCCTCCG
TCCCCCAGTCACTTCCCAGCCTGGCGGTCAGAGACTGGCTCGACGCCTCCCAGCAGCCCGACCACCAGGATTTCTACAGG
GTGTATGGGCAGCCGTCCACCAAACACTACGTGACGAGC

Alignment

ORF - retro_cjac_418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.86 %
• Parental protein coverage: 94.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HNFCRGCIGEAWAKDSGLVRCPECNQAYNQKPGLEKNLKLTNIVEKFNALHVEKPPAALHCVFCRRGPPL
          .NFCRGCIGEAWAKDSGLVR.PECNQAYNQKPGLEKNLKLTNI.EKFNALHVEKPP.ALHCVFCRR.PPL
Retrocopy NNFCRGCIGEAWAKDSGLVRFPECNQAYNQKPGLEKNLKLTNILEKFNALHVEKPPPALHCVFCRRCPPL

Parental  PAQKVCLRCEAPCCQSHVQTHLQQPSTARGHLLVEADDVRAWSCPQHNAYRLYHCEAEQVAVCQYCCYYS
          PAQKVCL.CE.PCCQSHVQ.HLQQPSTARGHLLVEADDVR.W.CPQHNAYRLYH.EAEQVAVCQYCCYYS
Retrocopy PAQKVCLCCEVPCCQSHVQMHLQQPSTARGHLLVEADDVRGWNCPQHNAYRLYHLEAEQVAVCQYCCYYS

Parental  GAHQGHSVCDVEIRRNEIRKMLMKQQDRLEEREQDIEDQLYKLESDKRLVEEKVNQLKEEVRLQYEKLHQ
          GAHQGHSV.DVEIRRN.IRKMLMKQQDRLEEREQDIEDQLYKLESDK.LVEEKVNQLKEEVRLQYEKLHQ
Retrocopy GAHQGHSVSDVEIRRNKIRKMLMKQQDRLEEREQDIEDQLYKLESDKLLVEEKVNQLKEEVRLQYEKLHQ

Parental  LLDEDLRQTVEVLDKAQ-AKFCSENAAQALHLGERMQEAKKLLGSLQLLFDKTEDVSFMKNTKSVKILMD
          LLDEDLRQTVEVLDKA..AKFCSENAAQALHLG..MQEAKKLLGSLQLLFDKTEDVSFMKN.KSVKILMD
Retrocopy LLDEDLRQTVEVLDKAR<AKFCSENAAQALHLGKHMQEAKKLLGSLQLLFDKTEDVSFMKNPKSVKILMD

Parental  RTQTCTGSSLSPPKIGHLNSKLFLNEVAKKEKQLRKMLEGPFSTPVPFLQSVPLYPCGVSSSGAEKRKHS
          RTQTCTGSSLSPPKIGHLNSKLFLN.VAKKEKQLRKMLEGPFST.VPFLQSVPLY.CGVSSSGAEKRKHS
Retrocopy RTQTCTGSSLSPPKIGHLNSKLFLNQVAKKEKQLRKMLEGPFSTLVPFLQSVPLYSCGVSSSGAEKRKHS

Parental  TAFPEASFLETSSGPVGGQYGAAGTASSEGQSGQPLGPCSSTQHLVALPGGAQPVHSSPVFPPSQYPNGS
          TAFPEASFLE..SGPVGGQY.AAGTAS.EGQSGQPLGPCSSTQHLVALPGGAQPVHSSPVF..SQYPNGS
Retrocopy TAFPEASFLEMLSGPVGGQYRAAGTASGEGQSGQPLGPCSSTQHLVALPGGAQPVHSSPVFLSSQYPNGS

Parental  AAQQPMLPQYGGRKILVCSVDNCYCSSVANHGGHQPYPRSGHFPWTVPSQEYSHPLPPTPSVPQSLPSLA
          AAQQPMLPQYGGRK.LVCSVDNCYC.SVANHGGHQPYPRSGHF.WTVPSQEYSHPLPPTPSVPQSLPSLA
Retrocopy AAQQPMLPQYGGRKTLVCSVDNCYCFSVANHGGHQPYPRSGHFLWTVPSQEYSHPLPPTPSVPQSLPSLA

Parental  VRDWLDASQQPGHQDFYRVYGQPSTKHYVTS
          VRDWLDASQQP.HQDFYRVYGQPSTKHYVTS
Retrocopy VRDWLDASQQPDHQDFYRVYGQPSTKHYVTS

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	0.11 RPM	8.45 RPM
SRP051959_heart	0.19 RPM	12.28 RPM
SRP051959_kidney	0.11 RPM	24.29 RPM
SRP051959_liver	0.11 RPM	6.06 RPM
SRP051959_lung	0.18 RPM	19.46 RPM
SRP051959_lymph_node	0.18 RPM	16.73 RPM
SRP051959_skeletal_muscle	0.24 RPM	5.96 RPM
SRP051959_spleen	0.36 RPM	12.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_418 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_418 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	ENSCJAG00000018057	1 retrocopy	retro_cjac_418 ,
Xenopus tropicalis	ENSXETG00000007381	1 retrocopy	retro_xtro_14,