RetrogeneDB ID: retro_cjac_1916

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:64025012..64025630(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031550
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDLIM2
• Ensembl ID: ENSCJAG00000020226
• Aliases: None
• Description: PDZ and LIM domain 2 (mystique) [Source:HGNC Symbol;Acc:13992]

Sequence

>retro_cjac_1916
GCCACAGTTTCCAGAGCGTGGCGTGTTCCCCAGGCCTCCTTGCCGCTGACCGCCTGTCCTACTCGAGCCCCCCCTACCAC
CCCTGGAAGCCAACAGGCAGGCCTCGGCCGCGCTGGTGACTCAGCGGTGCTGGAGCTGCCGCCTTCCCCGGGCCCTGGCC
TTTGTTCCTCCAGGCGCAGCGTGAACTTGGAAGGGGGCAGCCTCCTCCTGGACGAGGACTCGGAAGTCTTCAAGATGCTA
CAGGAAAATCATGAGGGAATGGGTGGCCCCCCGACAGTCCAGCTCCTTTCAGCTTTTGCAGGAAGCCCTGGAGGCTGAGG
AAAGAAGTGGCATGCCAGCCTTCCTGCCCAGCTTGCTGAGCCCTCAGTCCTCCCTGCCCGCCTCCAGGGCCCTGGCCACC
CTTCCAAGCTCCACACCTGTGAGAAGTGCAGCACCAGCACCGCGAACCAGGCCGTGCGCATCCAGGAGGGCTGGTACTGC
CACCCCGGCTGCTGCACCTGCACCGACTGTGGGCTGAACCTGAAGATGCGTGAGCACTTCTGGGTGGGCGAGGAGCTGTA
CTGTGAGAAACTTGCCTGCCAGCGCTACTCTGCACCCACTACCCTCAGCTCTGGGGCC

Alignment

ORF - retro_cjac_1916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 58.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAISRSFQSLVCSPGLPAADRLSYSSRPGSQQAGLGRAGDSAVLVLPPSPGPGPRSSRPSVNSEGGSLLL
          A..SR.......S..L.A.........PGSQQAGLGRAGDSAVL.LPPSPGPG..SSR.SVN.EGGSLLL
Retrocopy ATVSRAWRVPQASLPLTACPTRAPPTTPGSQQAGLGRAGDSAVLELPPSPGPGLCSSRRSVNLEGGSLLL

Parental  DEDSEVFKMLQENREGR-VAPRQSSSFRLLQEALEAEERGGTPAFLPSSLNPQSSLPTSRALAP-PPKLH
          DEDSEVFKMLQEN.EG..VAPRQSSSF.LLQEALEAEER.G.PAFLPS.L.PQSSLP.SRALA..P.KLH
Retrocopy DEDSEVFKMLQENHEGM>VAPRQSSSFQLLQEALEAEERSGMPAFLPSLLSPQSSLPASRALAT<PSKLH

Parental  TCEKCSTSIANQAVRIQEGRYRHPGCYTCADCGLNLKMRGHFWVGDELYCEKHARQRYSVPTPLSSRA
          TCEKCSTS.ANQAVRIQEG.Y.HPGC.TC.DCGLNLKMR.HFWVG.ELYCEK.A.QRYS.PT.LSS.A
Retrocopy TCEKCSTSTANQAVRIQEGWYCHPGCCTCTDCGLNLKMREHFWVGEELYCEKLACQRYSAPTTLSSGA

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	5.13 RPM
SRP051959_heart	0.00 RPM	4.21 RPM
SRP051959_kidney	0.00 RPM	8.74 RPM
SRP051959_liver	0.00 RPM	5.83 RPM
SRP051959_lung	0.00 RPM	14.19 RPM
SRP051959_lymph_node	0.00 RPM	14.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.14 RPM
SRP051959_spleen	0.00 RPM	22.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1916 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1916 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	ENSCJAG00000020226	1 retrocopy	retro_cjac_1916 ,