RetrogeneDB ID: retro_cjac_1098

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:48325586..48326745(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004305
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002950
• Aliases: None
• Description: None

Sequence

>retro_cjac_1098
CCAGAGATCATGTAGAGGGCCCTCATGGAGAGTGGGGCAGGGATGCCTGAGCAGGACAAGGACCCCAGAGTCCAAGAGAA
GCCCGATGATCAGAAAGGGGGCCCTGAGGGCACCAGGGATGCACGGTCTGCATTTAGACCCTTGCGGGACAGTGGAGGCC
TCTCTCCCTTCGTACCCAGGCCTGGGCCCCTGCAGAGAGATCTCCATACCCAGAGGTCAGAAATCCCATCTGACAAAGCA
TCCCAGCCCTCCGGGATGAGCTGCTGCGTCAAACACAATTCCATCTCCAGCTCCTACAGCTCCACAGGAGGCTTCCCGTG
GCTAAAGAGGAGGAAGGGGCCAGCCTCATCCCACTGCCGGCTGCCCCTCACTCCTTCAAAGGCAGTGAGTGAGGCCAGCC
CTCAGGCTGTCTCTCAGGGTCAGGCCCAGTGTGAAAAGGCAGCAGACGCAGCACCTGGGGAGAAACTGGCCCCCAGGAGT
GGCTCCCCGACATCTCAGGCCTCTAGTCCTCATAGACGAAAGTTCCCTCTGCTGCCACACAGGCGAGGGGAGCCTCTGAT
GCTGCCACCTCCCTTACAGCTGGGGTTCCAGGTCACCGCTGAAGACCTGGACCTGGAGAAAAATGCCGAAATTTTGTGGC
TAAACAGTGCACTGCAGGGTGAGGAAAAGTCCCTCTGGGAGTGCAGAGCCTCACTGCTTTCCCATGCTTTGTCCTCACCG
GCAACAGGGACATCTCTGCCTGCTGTCCCTAAAGCACCCAGCATGGATGCACAGCAGGAGAGATGCAAGTCTCAAGACGG
CCTGGACCCCGTGGCCCTCCAAGCACCTGCTGCAGGGCCCCCCTCTAGACCTGTCGGGGAGGAAGTGCAGGTCAGCAGGC
CCCCTGTTCTCCTCCTCAGACACCCTTTCTGCCATCTCTGCACACTCCTGGGACTCAGCCCAGGCCTCATCATCTGCTCC
AACACAGCCAGCCCAGGGCACCACAGAACACTCAGCCGCAGGGGCTTCCTTACCCACCACTTCCACCTCGAGCCCCCACA
CCAAAAGAAAGTCAACCTGGGCTGCAGACCTGGCTGGGAGCCTTCCTGACCCATCTTCTGCCTCTCCCACCACCACCCTG
GCCAGACCGAGGGTCAGTGGTCCCACCTCACTACGGAAA

Alignment

ORF - retro_cjac_1098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 93.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSRMLRALMESGAGMPEQDKDPRVQEKPDDQKGGPEGTRDAWSAFRPLRDSGGLSPFVSRPRPLQRDLHT
          P..M.RALMESGAGMPEQDKDPRVQEKPDDQKGGPEGTRDA.SAFRPLRDSGGLSPFV.RP.PLQRDLHT
Retrocopy PEIM*RALMESGAGMPEQDKDPRVQEKPDDQKGGPEGTRDARSAFRPLRDSGGLSPFVPRPGPLQRDLHT

Parental  QRSEIPSDKTSQPSGMSCCIKRNSIFSSYSSTGGFPWLKRRKGPASSHCRLPLTSSKTVSEVSPQAVSQG
          QRSEIPSDK.SQPSGMSCC.K.NSI.SSYSSTGGFPWLKRRKGPASSHCRLPLT.SK.VSE.SPQAVSQG
Retrocopy QRSEIPSDKASQPSGMSCCVKHNSISSSYSSTGGFPWLKRRKGPASSHCRLPLTPSKAVSEASPQAVSQG

Parental  QAQCEKAADSAPGEKPASRSGSLTSQASRPRRRKFPLLPRRRGEPLMLPSPLQLGFRVTAEDLNLEKNAE
          QAQCEKAAD.APGEK.A.RSGS.TSQAS.P.RRKFPLLP.RRGEPLMLP.PLQLGF.VTAEDL.LEKNAE
Retrocopy QAQCEKAADAAPGEKLAPRSGSPTSQASSPHRRKFPLLPHRRGEPLMLPPPLQLGFQVTAEDLDLEKNAE

Parental  IMCLNSALQGEEKSLWECRASLLSHALSSLATGTSSLPAVPKAPRTDAQQERCKSQDGLD-PMALKASAA
          I..LNSALQGEEKSLWECRASLLSHALSS.ATGTS.LPAVPKAP..DAQQERCKSQDGLD.P...K....
Retrocopy ILWLNSALQGEEKSLWECRASLLSHALSSPATGTS-LPAVPKAPSMDAQQERCKSQDGLD>PWPSKHLLQ

Parental  GSPSRPPVSGRKHKSAGPLFSSSDTLPATSAHSQDSAQASSFAPTQPAQGTTAYSAAGASLPTTSILSPC
          G.P.....SGRK..SAGPLFSSSDTL.A.SAHS.DSAQASS.APTQPAQGTT..SAAGASLPTTS..SP.
Retrocopy GPPL--DLSGRKCRSAGPLFSSSDTLSAISAHSWDSAQASSSAPTQPAQGTTEHSAAGASLPTTSTSSPH

Parental  TQRMLTWAADLAGSLPDPSSASPTTTLARQRVSGPTSLLK
          T.R..TWAADLAGSLPDPSSASPTTTLAR.RVSGPTSL.K
Retrocopy TKRKSTWAADLAGSLPDPSSASPTTTLARPRVSGPTSLRK

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.02 RPM	0.03 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1098 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1098 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002950	1 retrocopy	retro_cjac_1098 ,
Callithrix jacchus	ENSCJAG00000015967	2 retrocopies	retro_cjac_3482, retro_cjac_645,