RetrogeneDB ID: retro_cjac_4181

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:65737308..65738026(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf84
• Ensembl ID: ENSCJAG00000018418
• Aliases: None
• Description: chromosome 11 open reading frame 84 [Source:HGNC Symbol;Acc:25115]

Sequence

>retro_cjac_4181
ATGGCCCTAAAGGCTGAGGGCACTGCACCTGACTGCTTGAGGTGATGCTCAAATGTGAGGAAGGGGAGAATGAGAAGGAT
GCCATGGTTGTGGCCCTAATTCCACAGGTTTAGTTGATGTTAAGAGTGACCCAACAAGAGAAGACCTGACTGCCTAGACC
CAGCCCTCTGGAGGTGGGCAGCAATGACTGTGAGGAGCCCAAGCAGCATGTGTCTTGGGACCAGGAGTTTCTGGTGGGCA
GCAGCCCAAGATGAAGTGGGCCTGCACTGTGCATGGTGTGTGGCACTGAGATCCTGGCACCCTCAGCTGACGTGGCTTAC
TAGCACATCCTGGAGCAGCATCCTCACAGTGTGGACTTGAGTCCTTCCAAGAAGAACAACATCCTGGAGACCTGGAGTGA
AGGGGTGGCTCTCTTGCAAGACGTCAGAGCTGAGCAGTCGTCCACACCCAACTCAGACTCAGGCCAGGATGCCCAACTAG
ACCCAGACTCTAACCCAGACTCTGGCAGAATGCCAGCTGAAATTGTCATTCTCCTGGACTCTGAGAATAACCCATCCCTC
CCTTAAAGGAGCCAACCCAGGGGATTCTGTCTCCTCAAGCTTCTTGCTGCCCTTGCCACAGAGCCAGGAAATAAGAAGCC
CTGTGGTCAGAGATGGAAGCCCCCAGGGGGCGAGGAAGCCAGAAAGAAAAGAGGCAGACCATGACCAAAGACCTGGAC

Alignment

ORF - retro_cjac_4181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 63.25 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVKAEGAALDCF-EVTLKCEEGEDEEEAMVGPYSARPEPMLRVTQQEKTPPPRSSPLEAGSDSCEEPKQ
          MA.KAEG.A.DC..EV.LKCEEGE.E..AMV.........MLRVTQQEKT..PR.SPLE.GS..CEEPKQ
Retrocopy MALKAEGTAPDCL<EVMLKCEEGENEKDAMVVALIPQV*LMLRVTQQEKT*LPRPSPLEVGSNDCEEPKQ

Parental  QVSWEQEFLVGSSPGGSGRALCMVCGAEIRAPSADTARSHILEQHPHTLDLSPSEKSNILEAWSEGVALL
          .VSW.QEFLVGSSP..SG.ALCMVCG.EI.APSAD.A..HILEQHPH..DLSPS.K.NILE.WSEGVALL
Retrocopy HVSWDQEFLVGSSPR*SGPALCMVCGTEILAPSADVAY*HILEQHPHSVDLSPSKKNNILETWSEGVALL

Parental  QDIRAEQPSPPHSDSGQDAHPDPDSNPDPARVPAEIVVLLDSEDNPSLPKRSRPRGLRPLELPAVPATEP
          QD.RAEQ.S.P.SDSGQDA..DPDSNPD..R.PAEIV.LLDSE.NPSLP.RS.PRG...L.L.A..ATEP
Retrocopy QDVRAEQSSTPNSDSGQDAQLDPDSNPDSGRMPAEIVILLDSENNPSLP*RSQPRGFCLLKLLAALATEP

Parental  GNKKPRGQRWKEPAGEEPVRKKRGRP-MTKNLD
          GNKKP.GQRWK.P.GEE..RKKRGRP.MTK.LD
Retrocopy GNKKPCGQRWKPPGGEE-ARKKRGRP<MTKDLD

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	0.42 RPM	0.58 RPM
SRP051959_heart	1.28 RPM	1.88 RPM
SRP051959_kidney	0.87 RPM	0.98 RPM
SRP051959_liver	0.56 RPM	0.71 RPM
SRP051959_lung	1.33 RPM	3.46 RPM
SRP051959_lymph_node	0.37 RPM	4.41 RPM
SRP051959_skeletal_muscle	0.50 RPM	0.92 RPM
SRP051959_spleen	0.99 RPM	1.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4181 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4181 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
Canis familiaris	ENSCAFG00000015053	1 retrocopy	retro_cfam_753,
Callithrix jacchus	ENSCJAG00000018418	1 retrocopy	retro_cjac_4181 ,