RetrogeneDB ID: retro_cpor_198

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:7249313..7249781(+)
• Located in intron of: ENSCPOG00000025291

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF141
• Ensembl ID: ENSCPOG00000007808
• Aliases: None
• Description: None

Sequence

>retro_cpor_198
ATGGGACAGAATATTTCAGATGAGACACAGCTGGTTATTAACAAGTTACCAGAAAAAGAGTAGCAAAACATGTCACATTG
TTTAGAGAAAGTAGCTTCTTCACTTATGATTTCTTGGGTGAGTGGCTAAACTCAGTGAATGTAATAGATAAAATGGCCAC
TGGCCAGGAAAAGCATCTTCTCTTGGAGAGACAACCTGGTCTTGGTTCCTCTCCCTTTTGGAAAGTGGTGGTATGGATGA
TCTGTTCCAAGACTGAAAAAAGCAGTGACATTGTAGAAGCATCACAGATCATGAAGAGGTGCTAGTTCATTCAGCTTTAT
AAAGAAATCACAAGTCAAGCAGCAGGAGTGTGGCCTCAGAGCTTCACCTCTGAGGAATCTGGGAAAACTTATTCTCTGTG
ACATCTTGTCAGGCTGGCCTTGGGACGGCAAGAGGAAGCAGCTGACTGGTGAGGACGAGTGTGGTATC

Alignment

ORF - retro_cpor_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.75 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGQQISDQTQLVINKLPEKVAKHVTLIRE-SSSLTYEEFLGRVAELNDVTAKIAAGQEKHLLFEVQPGSD
          MGQ.ISD.TQLVINKLPEK.........E..SS.....FLG.......V..K.A.GQEKHLL.E.QPG..
Retrocopy MGQNISDETQLVINKLPEKE*QNMSHCLE<ESSFFTYDFLGEWLNSVNVIDKMATGQEKHLLLERQPGLG

Parental  SSALWKVVVRVVCTKINKSSGIVEASRIMNLYQFIQLYKDMTSQAAEVLAQSCTSEEPD-ENSSSVTSCQ
          SS..WKVVV...C.K..KSS.IVEAS.IM....FIQLYK..TSQAA.V..QS.TSEE...EN..SVTSCQ
Retrocopy SSPFWKVVVWMICSKTEKSSDIVEASQIMKRC*FIQLYKEITSQAAGVWPQSFTSEESG<ENLFSVTSCQ

Parental  ASL-WMGRVKQLTDEEECCI
          A.L.W.G..KQLT.E.EC.I
Retrocopy AGL<WDGKRKQLTGEDECGI

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	0.98 RPM	19.33 RPM
SRP017611_kidney	0.31 RPM	18.53 RPM
SRP017611_liver	0.00 RPM	7.14 RPM
SRP040447_lung	0.45 RPM	18.99 RPM
SRP040447_skeletal_muscle	0.04 RPM	7.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_198 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_198 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011014	1 retrocopy	retro_cjac_3999,
Cavia porcellus	ENSCPOG00000007808	2 retrocopies	retro_cpor_175, retro_cpor_198 ,
Macropus eugenii	ENSMEUG00000014558	1 retrocopy	retro_meug_1251,
Mus musculus	ENSMUSG00000030788	1 retrocopy	retro_mmus_2996,
Oryctolagus cuniculus	ENSOCUG00000002807	1 retrocopy	retro_ocun_1507,
Otolemur garnettii	ENSOGAG00000001765	1 retrocopy	retro_ogar_1262,
Sarcophilus harrisii	ENSSHAG00000002101	2 retrocopies	retro_shar_148, retro_shar_694,
Ictidomys tridecemlineatus	ENSSTOG00000019740	1 retrocopy	retro_itri_1573,