RetrogeneDB ID: retro_cjac_2136

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:47721097..47722070(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002557
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SOX7
• Ensembl ID: ENSCJAG00000004168
• Aliases: None
• Description: None

Sequence

>retro_cjac_2136
ATGTCGTTGCTGGCTGAGCGTCAGCGGAAGCAGAAGTGGGCTGTGGATCCTCAGAACACTGCCTGGAGTAACGACGATCC
CAAGTTTGGCCAGAGGATGCTAGAGAAGGTGGGGTGGTCTAAAGGAAAGCGTTTAAGGGCTCAGGAGCAAGGAGCCACAG
ATCATATGAAAGTTAAAGTGAAAAATAACCACCTGGGACTCGGAGCCACCATCAACAACGAGGACCACTGGATTGCACAT
CAGGATGATTTTAATCAGCTTCTGGCCGAGCTGAACACTTGCCGTGGGCAGGAAACCGCAGACTCCTCAGACAAGAAGGA
AAAGAAAACTTTTAGCCTTGAGGAAATGTCCAAAATCTCCAAAAACCGTGTTCACTATATGAAATTCACAAAAGGGAAGG
ATCTATCATCTCAGAGCAAAACAGATTTTAACTGCATTTTTGGGAAAAGACAGAGTAAGAAGACTCCTGAGGGCGATGCC
ACTTCCTCAACTCCAGACGAGAACGAAAGCACGACAACCAGTTACTTCACCATCCAGGACTACTTTGCCCAGCGGACGGC
AGCACTGAAGAACAAGTCCCAGGTCCCAGATCCAGGGCCTGACCTTTCCGAGACTCAGGTGGATAGAAAACAGATGAAGA
AAAGAAGCAAAGAGGCAGCAGGTAAGGATGTGAAGAGTTCCCCGAAGCCGAAGGCCAAGGGGCATACAGAGGAAATTCCC
AAGAGGGACGAGGCCACGGGGCAGGGGGCCAAGAAGAAGAGTGCGGGGGAGCAGCTCAGAGGCCCCTGCTGGGACCTGGG
TTCCGAGACCTCTGCTCAGGATGCTGGGGACTGTGCGCAGGTGCCTGAGGGCCTAGACTTCATCCTGAAGCCCAAAAAGA
GGAGAGGGAAGAAAAAGCTGCAAAAGCCGGTAGATAGCGGAGGATGCTACTCCAGAAGAAGCGCCAGTGAAAAAGAAGAA
GAAAGATTTCAAA

Alignment

ORF - retro_cjac_2136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.4 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSMLAERRRKQKWAVDPQNTAWSNDDSRFGQRMLEKMGWSKGKGLGAQEQGATDHIKVQVKNNHLGLGAT
          MS.LAER.RKQKWAVDPQNTAWSNDD..FGQRMLEK.GWSKGK.L.AQEQGATDH.KV.VKNNHLGLGAT
Retrocopy MSLLAERQRKQKWAVDPQNTAWSNDDPKFGQRMLEKVGWSKGKRLRAQEQGATDHMKVKVKNNHLGLGAT

Parental  INNEDNWIAHQDDFNQLLAELNTCHGQETSDSSDKKEKKSFSLEEKSKISKNRVHYMKFTKGKDLSSRSK
          INNED.WIAHQDDFNQLLAELNTC.GQET.DSSDKKEKK.FSLEE.SKISKNRVHYMKFTKGKDLSS.SK
Retrocopy INNEDHWIAHQDDFNQLLAELNTCRGQETADSSDKKEKKTFSLEEMSKISKNRVHYMKFTKGKDLSSQSK

Parental  TDLDCVFGKRQSKKTPEGDASSSTPDENKSTTTSAFTIQEYFAQRMAALKNKPQVPDPGPDLSETQVDRK
          TD..C.FGKRQSKKTPEGDA.SSTPDEN.STTTS.FTIQ.YFAQR.AALKNK.QVPDPGPDLSETQVDRK
Retrocopy TDFNCIFGKRQSKKTPEGDATSSTPDENESTTTSYFTIQDYFAQRTAALKNKSQVPDPGPDLSETQVDRK

Parental  TMKKRNKEAAGKDVKRSPKPKAKRHTEENPKRDEAEEQGARKKSAGEQLRGPCWDAGSETSAQDAGDCTR
          .MKKR.KEAAGKDVK.SPKPKAK.HTEE.PKRDEA..QGA.KKSAGEQLRGPCWD.GSETSAQDAGDC..
Retrocopy QMKKRSKEAAGKDVKSSPKPKAKGHTEEIPKRDEATGQGAKKKSAGEQLRGPCWDLGSETSAQDAGDCAQ

Parental  PPEGQDVTLKPKKRRGK-KKLQKAVE-IVEDATPEEMPVQKKKKKKK
          .PEG.D..LKPKKRRGK..K..KA...I.EDATPEE.PV.KKKK..K
Retrocopy VPEGLDFILKPKKRRGK<EKAAKAGR<IAEDATPEEAPVKKKKKDFK

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	2.17 RPM
SRP051959_heart	0.00 RPM	6.51 RPM
SRP051959_kidney	0.00 RPM	3.28 RPM
SRP051959_liver	0.06 RPM	2.99 RPM
SRP051959_lung	0.00 RPM	10.30 RPM
SRP051959_lymph_node	0.00 RPM	3.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.81 RPM
SRP051959_spleen	0.02 RPM	3.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2136 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2136 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	ENSCJAG00000004168	1 retrocopy	retro_cjac_2136 ,
Gorilla gorilla	ENSGGOG00000008531	1 retrocopy	retro_ggor_2460,