RetrogeneDB ID: retro_cjac_1816

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:76570442..76572423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC13
• Ensembl ID: ENSCJAG00000018450
• Aliases: None
• Description: None

Sequence

>retro_cjac_1816
TCTGCCGAGTGCGGCGAGTCATCCTTTTTGAACTTCCATGACTCAGACTGTGAACCCAAGGGTTCACCACCCTGTGACTC
CTTGCTTTCCCTCAACACTGAAGAGATCCTAAGCCAGGCCAAGTCTATTGCAGAACAAAAGAGATTCCCATTTGCCACTG
ATAATGACAGCACAAATGAAGAGTTAGCTATTGCTTATGTCTTGATTGGCAGTGGTCTCTATGATGAAGCTACACAGCAT
TTTTCAACAATGCTTCAGGAGGAGCCTGATCTGGTTAATGCAATTTATGGTCGAGGGATAGCCTATGGAAAGAAGGAAAT
ACATGACATTAAGAATGCTGAGCTTGCTCTGTTCGAACTTACCCGAGTAATTACCTTGGAACCAGATCGTCCAGAGGCAT
TTGAGTAGTGACCAGAAATTTTGTCCCCTCTGGACGAATTAATGAAGCAGTGAATGACCTCACTAAAGCTATTCAACTGC
AGCCCTCAGCACGGGTTACAGACATTGGAGAACCCTGTACTTCATATCAGAGGACTATGCAACAGCCCATGAAGACTTTC
AGCAGTCCTTACAACTGAACAAAAACCATCCTATAGCTATGCTATACAAAGGTTTAACTGTCTTTCACAGAGGACTTCTG
AAGGAAGCTATTGAATCCTTCAAAGAAGCTTTGAAGCAGAAAAGTTGATTGTATTGATGCATATAAAAGTCTAGGACAGG
TCTATAGAGAACTGGGCAATTTTGAACCAGCCACAGAGGGCTTTCAAAAGGCATTGTTGCCCAACCAAAATCATGTGCAA
ACCCTCCAGCTCTGGGGAATGATACTCTACCACCACGGCAGCTTACAGGAAGCCCTGAAGAACTTTAAGCAGTGTCTGCA
ACTAGAGCCATATAATGAAGTGTGCCAGTATATGAAAGGCCTCAGACATGTTGCCATGGGACAGTTTTATGAAGGGATAA
AAGCACAAATGAAAGTTATGCTGAATGATCCTCTCCTAGGCCAGAAAGCTATCCCTGAGTATCTTAAAGTGAAGTATCTT
CGAGAATATTCTCGATATCTTCATGCACACCTTGATACCCCACTTACAGAATATAACATTGAAGTGGACCTGCCTGGAAG
CTTTAAGGACCATTGGAATAAAAATCTGCCCTTTCCTTATAGAAGACTATGAAGAACAGCCAGGGTTGCAACCCCACATA
AAAGATGTGTTACATCAAAATTTTGTGAGTTATAAGCCTGAAGTACAGGAGCTGATCTGTGTGGCTGATGATTTGGGATC
ACTGATGCAATATGAAACACCTGGTTTCCTGCCAAGCAAGAGAATACACAGAGCTATGGGTTTGGCTGCATTGGAGGTCA
TGCAAGCCATGCAACGTACATGGACCAACTCGAAATTTTGAATGAATGGAAAGACACGGTCGTTGCAGTGGAGAGACATG
TTTGACATTGCAGTTAAATGGAGAAGGATTGCTGACCCAGATCGCCCTGTGCTGTGGTTAGATCAAATGTCGCATGAAGT
CTTAGCAGAGGTTTTAACAACCACATCAATTTAATCAGGGGTCAGGTGATCAACATGAGATACCTGGAATATTTTGAGAA
AATACTTCATTTTATTAAAGATAGAATTCTTGTTTATCATGGAGCTAATAATCCTAAAAAACTGCTGGAAGTTCGATAAG
CCCTGGAAAAGGTACACAAAGTAGAAGACTTTCTTCCAATTATAAAGCAGTTTAATACTAAAATGAAGGATGGGTTCACC
ATGAACACAAAATTCCCAGCCTTAAAGATCAGGGGAAGGAGTATGATGGATTCACAATCACGATTACAAAAGACAAAGTT
GGCAATATATTATTTTCTGTGGAAACTCAAACCACAGAAGAAAGAACACAATTTTATCATGCTGAAGTAGATGCACTTTA
TAAAAATTTGACAGCAAAAGGAAAAGTATTGATTTATTCATCAGAATTTGGGAAGGCTGAT

Alignment

ORF - retro_cjac_1816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.97 %
• Parental protein coverage: 85.2 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NASLSESSFLNFHDSDCEPKGSPPCDSLLSLNTEKILSQAKSIAEQKRFPFATDNDSTNEELAIAYVLIG
          .A...ESSFLNFHDSDCEPKGSPPCDSLLSLNTE.ILSQAKSIAEQKRFPFATDNDSTNEELAIAYVLIG
Retrocopy SAECGESSFLNFHDSDCEPKGSPPCDSLLSLNTEEILSQAKSIAEQKRFPFATDNDSTNEELAIAYVLIG

Parental  SGLYDEAIRHFSTMLQEEPDLVSAIYGRGIAYGKKGLHDIKNAELALFELSRVITLEPDRPEVFEQRAEI
          SGLYDEA..HFSTMLQEEPDLV.AIYGRGIAYGKK..HDIKNAELALFEL.RVITLEPDRPE.FE...EI
Retrocopy SGLYDEATQHFSTMLQEEPDLVNAIYGRGIAYGKKEIHDIKNAELALFELTRVITLEPDRPEAFE**PEI

Parental  LSPL-GRINEAVNDLTKAIQLQPSARL-YRHRGTLYFISEDYATAHEDFQQSLELNKNQPIAMLYKGLTF
          LSPL.GRINEAVNDLTKAIQLQPSAR..YRH..TLYFISEDYATAHEDFQQSL.LNKN.PIAMLYKGLT.
Retrocopy LSPL<GRINEAVNDLTKAIQLQPSARV<YRHWRTLYFISEDYATAHEDFQQSLQLNKNHPIAMLYKGLTV

Parental  FHRGLLKEAIESFKEALKQ-KVDFIDAYKSLGQAYRELGNFEAATESFQKALLLNQNHVQTLQLRGMMLY
          FHRGLLKEAIESFKEALKQ.KVD.IDAYKSLGQ.YRELGNFE.ATE.FQKALL.NQNHVQTLQL.GM.LY
Retrocopy FHRGLLKEAIESFKEALKQ>KVDCIDAYKSLGQVYRELGNFEPATEGFQKALLPNQNHVQTLQLWGMILY

Parental  HHGSLQEALKNFKRCLQLEPYNEVCQYMKGLSHVAMGQFYEGIKAQTKVMLNDPLPGQKASPEYLKVKYL
          HHGSLQEALKNFK.CLQLEPYNEVCQYMKGL.HVAMGQFYEGIKAQ.KVMLNDPL.GQKA.PEYLKVKYL
Retrocopy HHGSLQEALKNFKQCLQLEPYNEVCQYMKGLRHVAMGQFYEGIKAQMKVMLNDPLLGQKAIPEYLKVKYL

Parental  RAEYSRYLHAHLDTPLTEYNIDMDLPGSFKDHWAKNL-PFLIEDYEEQPGLQPHIKDVLHQNFESYKPEV
          R.EYSRYLHAHLDTPLTEYNI..DLPGSFKDHW.KNL.PFLIEDYEEQPGLQPHIKDVLHQNF.SYKPEV
Retrocopy R-EYSRYLHAHLDTPLTEYNIEVDLPGSFKDHWNKNL>PFLIEDYEEQPGLQPHIKDVLHQNFVSYKPEV

Parental  QELICVADRLGSLMQYETPGFLPNKRIHRAMGLAALEVMQAVQRTWTNSKVRMNGKTRLMQWRDMFDIAV
          QELICVAD.LGSLMQYETPGFLP.KRIHRAMGLAALEVMQA.QRTWTNSK..MNGKTR..QWRDMFDIAV
Retrocopy QELICVADDLGSLMQYETPGFLPSKRIHRAMGLAALEVMQAMQRTWTNSKF*MNGKTRSLQWRDMFDIAV

Parental  KWRRIADPDQPVLWLDQMP-ARSLSRGFNNHINLIRGQVINMRYLEYFEKILHFIKDRILVYHGANNPKG
          KWRRIADPD.PVLWLDQM..A.SLSRGFNNHINLIRGQVINMRYLEYFEKILHFIKDRILVYHGANNPK.
Retrocopy KWRRIADPDRPVLWLDQMS<A*SLSRGFNNHINLIRGQVINMRYLEYFEKILHFIKDRILVYHGANNPKK

Parental  LLEVREALEKVHKVEDLLPIMKQFNTKTKDGFTVNT-KVPSLKDQGKEYDGFTITITGDKVGNILFSVET
          LLEVR.ALEKVHKVED.LPI.KQFNTK.KDGFT.NT.K.PSLKDQGKEYDGFTITIT.DKVGNILFSVET
Retrocopy LLEVR*ALEKVHKVEDFLPIIKQFNTKMKDGFTMNT<KIPSLKDQGKEYDGFTITITKDKVGNILFSVET

Parental  QTTEERTQLYHAEIDALYKDLTAKGKVLILSSEFGEAD
          QTTEERTQ.YHAE.DALYK.LTAKGKVLI.SSEFG.AD
Retrocopy QTTEERTQFYHAEVDALYKNLTAKGKVLIYSSEFGKAD

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	0.07 RPM	9.39 RPM
SRP051959_heart	0.04 RPM	6.60 RPM
SRP051959_kidney	0.09 RPM	9.05 RPM
SRP051959_liver	0.06 RPM	6.45 RPM
SRP051959_lung	0.03 RPM	10.61 RPM
SRP051959_lymph_node	0.05 RPM	17.65 RPM
SRP051959_skeletal_muscle	0.04 RPM	7.58 RPM
SRP051959_spleen	0.06 RPM	12.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1816 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1816 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	ENSCJAG00000018450	1 retrocopy	retro_cjac_1816 ,