RetrogeneDB ID: retro_cjac_3204

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:32688146..32689730(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNC1I2
• Ensembl ID: ENSCJAG00000007196
• Aliases: None
• Description: dynein, cytoplasmic 1, intermediate chain 2 [Source:HGNC Symbol;Acc:2964]

Sequence

>retro_cjac_3204
GTCCCTCCTCCTATGTCTCCATCTTCCAAATCTGTGAGCACTCCAAGTGAAACTGGAAGCCAGGACTCTGGAGATGGTGC
CATGGGATCTAGGATGCTGCATTGGGATACAGATCCATCAGTTCTTCAGCTTCACTCAGATTCCGATTTGGGAAGAGGAC
CTATTAAACTTGGAATGGCTAAAATCACTCAAGTCAATTTTCCTCCTTGAGAAATTTTCACATATACAATGGAAACTCAG
ACTCCAGTTATGCCTCAACCCAAAGAAGATGAAGAGGAAAATGATGATGTAGTGGCTCCTAAACCACCTATTGAACCCAA
AGAAGAGAAAACTTTGAAGAAAGAAGAGGAAAATGATAGTAAAGCTCCCCCTCATGAGCTGACTGAAGAATAAAAGCAAC
AAATCTTACACTCTGAGGAATTTTTAAGTTTCTTTGACCATTCTACAAGAATTGTAGAAAGAGCTCTTTCTGAGCAGATT
AACATCTTCTTTGACTACAGTGGGAGAGATTTGGAAGACAAAGAAGGAGAGATTCAAGCAGGTGCTAAACTGTCAATAAA
TTGACAATTTTTTGATGAAAGATGGTCAAAACATCGAGTTGTTAGTTGTTTGGATTGGTCATCTCAGTATCCAGAGTTAC
TCGTGGCTTCCTATAATAACAATGAAGATGCCTCTCATGAGCCCGATGGTGTGGCCCTTGTTTGGAATATGAAATACAAA
AAAACTACCCCAGGGTATGTGTTTCACTGCCAGTTAGCTGTGATGTCTGCCACATTTGCAAAATTTCATCCAAATCTTGT
TGGTGGTGGTACATATTCAGGCCGGATTGTGCTTTGGGATAACCGTAGCAATGAAAGAACTCCAGTGCAAAGAACTCCAC
TGTCAGCAGCTGCACACACACACCCTGTATATTGTGTAAATGTTGTTGGAACACAAAATGCTCACAATCTGATTAGCATC
TCTACTGATGGAAAAATTTGTTCATGGAGTCTGGACATGCTTTCCCATCCACAGGATAGCATGGAGTTGGTTCATAAACA
ATCAAAGGCAGTAGCTGTGACATCCATGTCCTTCCCTGTTGGAGATGTCAACAACTTTGTTGTTGGGAGTGAAGAAGTTT
CAGTGTACACAGCATGCTGCCATGGCAGCAAAGCTGGAATCAGTGAGATGTTTGAGGGGCATCAAGGACCAATCACTGGC
ATCCATTGTCATGCAGCTGTTGGAGCAGTAGACTTCTTACTTTTTTTTGTCACTTCATCATTTGACTGGACAGTAAAACT
TTGGACAACTAAGAATAACAAGCCTTTGTATTCATTTGAAGATAATTCAGACTATGTTTATGATGTTATGTGGTCACCCA
CTCACCCAGCCTTGTTTGCCTGTGTGGATGGCATGGGAAGATTGGATTTGTGGAATCTCAATAATGACACAGAGGTACCA
ACTGCCAGCATTTCTGTGGAGGGTAATCCTGCTCTTAATCTTGTGAGATGGACCCATTCTGGCAGAGAGATTGCTGTTGG
TGATTCTGAAGGACAGATTGTTATATATGATGTGGGACAGCAGATCGCCATTCCCCAAAATGAT

Alignment

ORF - retro_cjac_3204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 82.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRTLHWDTDPSVLQLHSDSDLGRGPIKLGMAKITQVDFPPR
          VPPPMSPSSKSVSTPSE.GSQDSGDGA.GSR.LHWDTDPSVLQLHSDSDLGRGPIKLGMAKITQV.FPP.
Retrocopy VPPPMSPSSKSVSTPSETGSQDSGDGAMGSRMLHWDTDPSVLQLHSDSDLGRGPIKLGMAKITQVNFPP*

Parental  EIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPPHELTEEEKQQILHSEE
          EI.TYT.ETQTPVM.QPKEDEEE.DDVVAPKPPIEP.EEKTLKK.EENDSKAPPHELTEE.KQQILHSEE
Retrocopy EIFTYTMETQTPVMPQPKEDEEENDDVVAPKPPIEPKEEKTLKKEEENDSKAPPHELTEE*KQQILHSEE

Parental  FLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERWSKHRVVSCLDWSSQY
          FLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLS.N.QFFDERWSKHRVVSCLDWSSQY
Retrocopy FLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSIN*QFFDERWSKHRVVSCLDWSSQY

Parental  PELLVASYNNNDDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWD
          PELLVASYNNN.DA.HEPDGVALVWNMKYKKTTP.YVFHCQ.AVMSATFAKFHPNLV.GGTYSG.IVLWD
Retrocopy PELLVASYNNNEDASHEPDGVALVWNMKYKKTTPGYVFHCQLAVMSATFAKFHPNLVGGGTYSGRIVLWD

Parental  NRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKA
          NRSN.RTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKA
Retrocopy NRSNERTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKA

Parental  VAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSS
          VAVTSMSFPVGDVNNFVVGSEE.SVYTAC.HGSKAGISEMFEGHQGPITGIHCHAAVGAVDF...FVTSS
Retrocopy VAVTSMSFPVGDVNNFVVGSEEVSVYTACCHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFLLFFVTSS

Parental  FDWTVKLWTTKNNKPLYSFEDNSDYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASISVEGNP
          FDWTVKLWTTKNNKPLYSFEDNSDYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASISVEGNP
Retrocopy FDWTVKLWTTKNNKPLYSFEDNSDYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASISVEGNP

Parental  ALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRND
          ALN.VRWTHSGREIAVGDSEGQIVIYDVG.QIA.P.ND
Retrocopy ALNLVRWTHSGREIAVGDSEGQIVIYDVGQQIAIPQND

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	0.09 RPM	41.05 RPM
SRP051959_heart	0.04 RPM	41.54 RPM
SRP051959_kidney	0.07 RPM	42.62 RPM
SRP051959_liver	0.09 RPM	24.84 RPM
SRP051959_lung	0.15 RPM	50.22 RPM
SRP051959_lymph_node	0.05 RPM	34.34 RPM
SRP051959_skeletal_muscle	0.02 RPM	22.43 RPM
SRP051959_spleen	0.04 RPM	46.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3204 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007196	1 retrocopy	retro_cjac_3204 ,
Homo sapiens	ENSG00000077380	1 retrocopy	retro_hsap_574,
Tursiops truncatus	ENSTTRG00000011355	1 retrocopy	retro_ttru_237,