RetrogeneDB ID: retro_cpor_1019

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:38517571..38517833(+)
• Located in intron of: ENSCPOG00000026679

Retrocopy information

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

Parental gene information

• Parental gene symbol: C8ORF40
• Ensembl ID: ENSCPOG00000002665
• Aliases: None
• Description: None

Sequence

>retro_cpor_1019
ATTGATTATGCAGTTCATGAAGCCTGGCATGATACCACCAACGTTTACCTAATAGTGGTCCTTTCATTCTCTTCATGTAG
GCCAAAGAATCAAAGGAAAATTATGAGGATATTCAGTGTTGCACCTACAAGGAACTTTGTCAGAGCCCAATTTTTATGAT
GCAATGAGCAAAGTTCACTTAAGATAACCGCATATGTATTCCATTTCAAGAAAGTATGAGTGTCTGCAACTACAAAGCCA
AGCTGACAGTGTACAGCTCTCT

Alignment

ORF - retro_cpor_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.57 %
• Parental protein coverage: 92.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDYTVHEAWNEATNVYLIVILVSFGLFLYAKRNKRRIMRIFSVPPT-KE-TLTEPNFYDTMSKIRLRQQL
          .DY.VHEAW...TNVY.....V..........N.R.IMRIFSV.PT.KE.TL.EPNFYD.MSK..LR...
Retrocopy IDYAVHEAWHDTTNVY---LIVVLSFSSCRPKNQRKIMRIFSVAPT<KE<TLSEPNFYDAMSKVHLR*P-

Parental  EMYSISRKYDYQQPQNQADSVQLS
          .MYSISRKY...Q.Q.QADSVQLS
Retrocopy HMYSISRKYECLQLQSQADSVQLS

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	15.53 RPM
SRP017611_kidney	0.00 RPM	37.69 RPM
SRP017611_liver	0.00 RPM	50.40 RPM
SRP040447_lung	0.00 RPM	15.69 RPM
SRP040447_skeletal_muscle	0.00 RPM	42.34 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1019 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1019 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005067	1 retrocopy	retro_amel_346,
Cavia porcellus	ENSCPOG00000002665	1 retrocopy	retro_cpor_1019 ,
Felis catus	ENSFCAG00000031243	1 retrocopy	retro_fcat_1312,
Pteropus vampyrus	ENSPVAG00000014829	1 retrocopy	retro_pvam_282,
Sorex araneus	ENSSARG00000008851	2 retrocopies	retro_sara_28, retro_sara_510,
Tupaia belangeri	ENSTBEG00000008608	1 retrocopy	retro_tbel_2485,