RetrogeneDB ID: retro_cjac_891

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:15810171..15810727(-)
• Located in intron of: ENSCJAG00000013130

Retrocopy information

• Ensembl ID: ENSCJAG00000013156
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HESX1
• Ensembl ID: ENSCJAG00000010981
• Aliases: None
• Description: HESX homeobox 1 [Source:HGNC Symbol;Acc:4877]

Sequence

>retro_cjac_891
ATGTCTCCCAGCCTTCAGGAAGGCGCTCAGCTCCGGGAAAGCAAACCCTCAACTTGCTCCTTTTCAATTGAGAGAATCTT
AGGAATGGACGAGAAGAAAGACTGTGTTCCATTAGTGAAACCCTACTGGCCCTGGGCAGACACCTGCAGCTCCTCAGGGC
AAGATGGTAACTTATGTCTATATGTCCCAAATCCTCCCAGTGGCATTTCATTCCCTAGCATGGTGGATCACCCAATACTA
GAAGAAAGAGCTTCAAAATATGAAAATTACTTTTCAGCCTCAGAAAGACTGTATTTGAAAAGAGAGTTGAGTTGGTATAG
AGGCCGAAGACCAAGAACTGCTTTTACTCAAAACCAGATTGAAGTGTTAGAAAATGTCTTTAGAGTAAACTGCTATCCTG
GCATTGATATTAGAGAAGACTTAGCTCAAAAATTGAATCTAGAGGAAGACAGAATCCAGATTTGGTTCCAAAATCGGCGT
GCAAAACTGAAAAGGTTCCCGTAGAAAATCACAGTTTCTAATGGCGAAAAAAAATTTCAACACAAATCTCCTGGAA

Alignment

ORF - retro_cjac_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSPSLQEGAQLRESKPSTCSFSIERILGMDEKKDCVPLVKPYWPWADTCSSSGKDGNLCLYVPNPPNGIS
          MSPSLQEGAQLRESKPSTCSFSIERILGMDEKKDCVPLVKPYWPWADTCSSSG.DGNLCLYVPNPP.GIS
Retrocopy MSPSLQEGAQLRESKPSTCSFSIERILGMDEKKDCVPLVKPYWPWADTCSSSGQDGNLCLYVPNPPSGIS

Parental  FPSMVDHPIPEERASKYENYFSASERLYLKRELSWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIRED
          FPSMVDHPI.EERASKYENYFSASERLYLKRELSWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIRED
Retrocopy FPSMVDHPILEERASKYENYFSASERLYLKRELSWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIRED

Parental  LARKLNLEEDRIQIWFQNRRAKLKR-SHRESQFLMAKKNFNTNLLE
          LA.KLNLEEDRIQIWFQNRRAKLKR.S.R.SQFLMAKKNFNTNLLE
Retrocopy LAQKLNLEEDRIQIWFQNRRAKLKR>SRRKSQFLMAKKNFNTNLLE

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	0.16 RPM	0.00 RPM
SRP051959_heart	0.04 RPM	0.09 RPM
SRP051959_kidney	0.02 RPM	0.04 RPM
SRP051959_liver	0.17 RPM	0.09 RPM
SRP051959_lung	0.44 RPM	0.16 RPM
SRP051959_lymph_node	0.43 RPM	0.18 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.09 RPM
SRP051959_spleen	0.48 RPM	0.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_891 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011722	1 retrocopy	retro_amel_862,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123,
Callithrix jacchus	ENSCJAG00000009866	1 retrocopy	retro_cjac_326,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891 ,
Callithrix jacchus	ENSCJAG00000018583	1 retrocopy	retro_cjac_1380,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Dasypus novemcinctus	ENSDNOG00000003677	1 retrocopy	retro_dnov_58,
Mustela putorius furo	ENSMPUG00000016854	2 retrocopies	retro_mputfur_112, retro_mputfur_174,