RetrogeneDB ID: retro_cjac_778

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:41464045..41464648(-)
• Located in intron of: ENSCJAG00000021021

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAGLN
• Ensembl ID: ENSCJAG00000012755
• Aliases: LOC100385619, TAGLN, transgelin
• Description: transgelin [Source:HGNC Symbol;Acc:11553]

Sequence

>retro_cjac_778
ATGGCCAACAAGGGTCCTTCCTATGGCATGAGCCGCGAAGTGCAGTCCAAAATCGAGAAGAAATAAGATGAGGAGCTGAA
AGAGCGGCTGGTGGAATGGATTATAGTGCAGTGTGGCACTGATGTGGGCCGCCCAGACCATGGGCGCCTGGGCTTCCAGG
TCTGGCTGAAGAATGGCGTGATTCTGAGCAAGCTGGTGAATAGCCTGTACCCTGATGGCTCCAAGCCAGTGAAGGTGCCT
GAGAACCTGCCCTCCATGGTCTTCAAGCAGATGGAGCAGGTGGCCCAGTTCCTGAAGGCAGCTGAGGACTATGGGGTCAC
CAAGACTGACATGTTCCAGACTGTTGACCTCTTTGAAGGCAAAGACAAGGCAGCAGTGCAGAGGACCCTGATGGCTTTGT
GCAGCTTGGCAGTGACCAAGAATGATGGGCACTACCATGGAGATCCCAACTGGTTTATGAAGAAAGCGCAGGAGCATAAG
AGAGAATTCACAGAGAGCCAGCTGCAGGAGGGAAAGCATGTCATTGGCCTTCAGATGGGCAGCAACAGAGGGGCCTCCCA
GGCTGGCATGACGGGCTATGGACGACCTCAGCAGATCATCAGT

Alignment

ORF - retro_cjac_778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANKGPSYGMSREVQSKIEKKYDEELEERLVEWIIVQCGPDVGRPDRGRLGFQVWLKNGVILSKLVNSLY
          MANKGPSYGMSREVQSKIEKK.DEEL.ERLVEWIIVQCG.DVGRPD.GRLGFQVWLKNGVILSKLVNSLY
Retrocopy MANKGPSYGMSREVQSKIEKK*DEELKERLVEWIIVQCGTDVGRPDHGRLGFQVWLKNGVILSKLVNSLY

Parental  PDGSKPVKVPENPPSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKDMAAVQRTLMALGSLAVTK
          PDGSKPVKVPEN.PSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKD.AAVQRTLMAL.SLAVTK
Retrocopy PDGSKPVKVPENLPSMVFKQMEQVAQFLKAAEDYGVTKTDMFQTVDLFEGKDKAAVQRTLMALCSLAVTK

Parental  NDGHYRGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRGASQAGMTGYGRPRQIIS
          NDGHY.GDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRGASQAGMTGYGRP.QIIS
Retrocopy NDGHYHGDPNWFMKKAQEHKREFTESQLQEGKHVIGLQMGSNRGASQAGMTGYGRPQQIIS

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	1.18 RPM	207.63 RPM
SRP051959_heart	1.18 RPM	344.51 RPM
SRP051959_kidney	0.64 RPM	30.53 RPM
SRP051959_liver	0.28 RPM	5.65 RPM
SRP051959_lung	0.94 RPM	44.44 RPM
SRP051959_lymph_node	0.73 RPM	22.15 RPM
SRP051959_skeletal_muscle	0.39 RPM	24.79 RPM
SRP051959_spleen	0.63 RPM	29.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_778 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_778 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Callithrix jacchus	ENSCJAG00000012755	2 retrocopies	retro_cjac_723, retro_cjac_778 ,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Microcebus murinus	ENSMICG00000002371	1 retrocopy	retro_mmur_666,
Oryctolagus cuniculus	ENSOCUG00000011970	1 retrocopy	retro_ocun_116,