RetrogeneDB ID: retro_cpor_1067

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_43:3566476..3566740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HESX1
• Ensembl ID: ENSCPOG00000012741
• Aliases: None
• Description: None

Sequence

>retro_cpor_1067
CACTAACATTACCTTTCAACCTCAGAAAGACTGTCTTTTAAAAGAGAGATGGGTTGGTATAGAGGACGAAGACCAAGAAC
TGCTTTTACTCAGAACCAGATTGAGGTACTGGAAAATGTCTTTAGAGTGAACTGCTATCCTGGCATTGATATCCGAGAAG
ACTTAGCTCAAAAATTGAATCTAGAGGAAGACATAATTCAGATTTGGTTCCAAAATCGTCGAGCAAGGCTGAAAAGGTCC
CACAGAGAATCACAGTTTTTAATG

Alignment

ORF - retro_cpor_1067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HEHYLSTSERLSLKREMGWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIREDLAQKLNLEEDRIQIWF
          H.HYLSTSERLS.KREMGWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIREDLAQKLNLEED.IQIWF
Retrocopy H*HYLSTSERLSFKREMGWYRGRRPRTAFTQNQIEVLENVFRVNCYPGIDIREDLAQKLNLEEDIIQIWF

Parental  QNRRAKLKRSHRESQFLM
          QNRRA.LKRSHRESQFLM
Retrocopy QNRRARLKRSHRESQFLM

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
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1067 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1067 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011722	1 retrocopy	retro_amel_862,
Canis familiaris	ENSCAFG00000007995	2 retrocopies	retro_cfam_1907, retro_cfam_954,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891,
Cavia porcellus	ENSCPOG00000003420	1 retrocopy	retro_cpor_149,
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,
Tupaia belangeri	ENSTBEG00000017505	1 retrocopy	retro_tbel_339,