RetrogeneDB ID: retro_cjac_2631

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:86113670..86114540(-)
• Located in intron of: ENSCJAG00000001233

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR25
• Ensembl ID: ENSCJAG00000016951
• Aliases: None
• Description: None

Sequence

>retro_cjac_2631
TCTGAGTTTATTCAGCCGTATTTGAACAGCCATTATAAAGAAACCACGGTTCCCCAGAAAGTGCTTTTCTACCTGAGAGG
CCACAGGGGCCCTGTCAACAGTGTTCAGTGGTGTCCAGTGCTTTCTCAGAGCCACATGCTTCTCTCCACTTCTATGGATA
AAACTTTCAAGGTATGGAACGCTGTGGACTCTGGGTACTGCCTGCAGACCTACTCCCTGCACACAGAGGCAGTGCGGGCC
GCCCGCTGGTCTCCCTGTGGCCGGCGCATCCTCAGTGGTGGCTTTGACTTCGCCCTGCATCTAACAGACCTTGAAACAGG
AACCCAGCTATTTAGTGGTCGAAGTGACTTTAGAATCACTACCTTGAAATTCCATCCAAAAGACCACAACATTTTTTTAT
GTGGAGGCTTCAGCTCTGAAATGAAAGCTTGGGATATAAGGACCAGCAAGGTGATGAGAAGCTACAAGGCCACCATTCAG
CAGACCTTGGACATCCTGTTCCTCCCGGAAGGCTCTGAGTTCCTGAGCAGCACGGATGCTTCCACCCGGGACTCGGCTGA
CCGCACCATTATTGCCTGGGATTTCCGGACCTCTGCCAAAATCTCTAATCAGATTTTCCTCGAGAGATTCACCTGCCCCA
GCCTCGCCTTGCACCCCAGGGAACCCGTGTTCCTGGCACAGACCAATGGCAACTACCTGGCCCTTTTCTCCACTGTGTGG
CCCTACCGGATGAGCAGACGGCGGCGCTATGAAGGGCACAAGGTGGAGGGCTACTCAGTGGGCTGCGAGTGTTCCCCAGG
CGGTGACCTGCTGGTGACGGGCAGCGCTGATGGCCGGGTCCTGATGTACAGCTTCCGCACAGCCAGCCGG

Alignment

ORF - retro_cjac_2631 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEFIQPYLNSHYKETTVPQKVLFYLRGHRGPVNSVQWCPVLSQSHMLLSTSMDKTFKVWNAVDSGYCLQT
          SEFIQPYLNSHYKETTVPQKVLFYLRGHRGPVNSVQWCPVLSQSHMLLSTSMDKTFKVWNAVDSGYCLQT
Retrocopy SEFIQPYLNSHYKETTVPQKVLFYLRGHRGPVNSVQWCPVLSQSHMLLSTSMDKTFKVWNAVDSGYCLQT

Parental  YSLHTEAVRAARWSPCGRRILSGGFDFALHLTDLETGTQLFSGRSDFRITTLKFHPKDHNIFLCGGFSSE
          YSLHTEAVRAARWSPCGRRILSGGFDFALHLTDLETGTQLFSGRSDFRITTLKFHPKDHNIFLCGGFSSE
Retrocopy YSLHTEAVRAARWSPCGRRILSGGFDFALHLTDLETGTQLFSGRSDFRITTLKFHPKDHNIFLCGGFSSE

Parental  MKAWDIRTSKVMRSYKATIQQTLDILFLREGSEFLSSTDASTRDSADRTIIAWDFRTSAKISNQIFXERF
          MKAWDIRTSKVMRSYKATIQQTLDILFL.EGSEFLSSTDASTRDSADRTIIAWDFRTSAKISNQIF.ERF
Retrocopy MKAWDIRTSKVMRSYKATIQQTLDILFLPEGSEFLSSTDASTRDSADRTIIAWDFRTSAKISNQIFLERF

Parental  TCPSLALHPREPVFLAQTNGNYLALFSTVWPYRMSRRRRYEGHKVEGYSVGCECSPGGDLLVTGSADGRV
          TCPSLALHPREPVFLAQTNGNYLALFSTVWPYRMSRRRRYEGHKVEGYSVGCECSPGGDLLVTGSADGRV
Retrocopy TCPSLALHPREPVFLAQTNGNYLALFSTVWPYRMSRRRRYEGHKVEGYSVGCECSPGGDLLVTGSADGRV

Parental  LMYSFRTASR
          LMYSFRTASR
Retrocopy LMYSFRTASR

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	0.35 RPM	3.00 RPM
SRP051959_heart	0.30 RPM	1.75 RPM
SRP051959_kidney	0.47 RPM	2.64 RPM
SRP051959_liver	0.30 RPM	3.08 RPM
SRP051959_lung	0.75 RPM	2.75 RPM
SRP051959_lymph_node	0.39 RPM	3.54 RPM
SRP051959_skeletal_muscle	0.35 RPM	2.40 RPM
SRP051959_spleen	0.34 RPM	2.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2631 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2631 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	ENSCJAG00000016951	1 retrocopy	retro_cjac_2631 ,