RetrogeneDB ID: retro_cpor_197

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:72996759..72997922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSCPOG00000002525
• Aliases: None
• Description: None

Sequence

>retro_cpor_197
GAACAAACGAGGCCCCTGAGACCTAGCTCACAGGATAAAACCCCACAGCAGAACTCAGAGTCAGCAAAGGCTAAGCCCCA
GGTGGTTGTGACTCCTGTGTTAATGTTTAAGCTGTCTGCCAACGCCCCCAAATTTTACCCATCAGGTTATTCTGCTTATA
CAGAATCCTATGAAGATGGTTGTGAGGATTATCCCACTCTATCAGACTATGTTCAAGAGTTTTTGAATCATCTTACAGAG
CAACCTGGCAGTTTTGAAACTGAAATTGAACAATTTGCAGAGACCCTGAATGGCTGGGTTACAACTGATGATGCTTTGCA
AGAACTTGTGGAACTCATCTACCAACAGGCCACATCTATCCCAAACTTCTCTTACATGGGAGCTCGCCTGTGTAATTACC
TGTCCCATCATCTGACAATTAGTCCACAGAGTGGCAACTTCCACCAATTGCTACTTCAAAGATGTCGGACTGAATATGAA
GTTAAAGATGAAGCTGCGAAAGGAGATGAAGTGACTCGAAAGTGATTTCATGCATTTGTACTCTTTCTGGGAAAACTTTA
TCTTAACCTGGAGATCAAGGGAACAAATGGGCAGGTTACGAGAGCAGATATTCTTCAAGTTGGTCTGCGGGAATTGTTGA
ATGCCTTGTTCTCTAATCCAATGGATGACAACTTAATTTGTGCAGTAAAATTATTAAAGTTACAAGACCAGTTTTGGAAG
ATGCTTGGAAAGAAAAATTAAAGACTGATATGGAAGAAATTATTCAGAGAATTGAAAATGTTGTCCTAGATGCAAACTGC
AGCATAGATGTAAAACAGATGCTCTTGAAGCTTGTAGAACTCCAGTCAAGTAACTGGGGCAGAGTACATGCAACTTTAAC
GTACAGAAAAGCAACACCTGAAAATGACCCTACCTACTTTATGAATGAACCAACATTTTATACATCTGATGGTGTACCTT
TCACTGCAGCAGATCCAGATTACCAAGAGAAGTATCAAGAGTTACTTGAAAGAGAGGACTTTTTTCCAGATTATGAAGAA
AATGGAACAGATTTATCAGGGGCTGGTGAGCCATACTTGGATGATATTGATGATGAGATGGACCCAGAAATTGAAGAAGC
TTATGAAAAGTCTTGTTTGGAATCAGAGCATAAGCGAAAACAG

Alignment

ORF - retro_cpor_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.86 %
• Parental protein coverage: 92.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQTRPLRAPPSSQDKTPQQNSESAMAKPQVVVAPVLMSKLSANAPEFYPSGYSAYTESYEDGCEDYPTLS
          EQTRPLR..PSSQDKTPQQNSESA.AKPQVVV.PVLM.KLSANAP.FYPSGYSAYTESYEDGCEDYPTLS
Retrocopy EQTRPLR--PSSQDKTPQQNSESAKAKPQVVVTPVLMFKLSANAPKFYPSGYSAYTESYEDGCEDYPTLS

Parental  DYVQEFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHL
          DYVQEFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHL
Retrocopy DYVQEFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHL

Parental  TISPQSGNFRQLLLQRCRIHHKVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVG
          TISPQSGNF.QLLLQRCR....VKD.AAKGDEVTRK.FHAFVLFLG.LYLNLEIKGTNGQVTRADILQVG
Retrocopy TISPQSGNFHQLLLQRCRTEYEVKDEAAKGDEVTRK*FHAFVLFLGKLYLNLEIKGTNGQVTRADILQVG

Parental  LRELLNALFSNPMDDNLICAVKLLKL-TGSVLEDAWKEKLKTDMEEIIQRIENVVLDANCSRDVKQMLLK
          LRELLNALFSNPMDDNLICAVKLLKL.T..VLEDAWKEKLKTDMEEIIQRIENVVLDANCS.DVKQMLLK
Retrocopy LRELLNALFSNPMDDNLICAVKLLKL<TRPVLEDAWKEKLKTDMEEIIQRIENVVLDANCSIDVKQMLLK

Parental  LVELRSSNWGRVHATSTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEE
          LVEL.SSNWGRVHAT.TYR.ATPENDP.YFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEE
Retrocopy LVELQSSNWGRVHATLTYRKATPENDPTYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEE

Parental  NGTDLSGAGDPYLDDIDDEMDPEIEEAYEKFCLESEHKRKQ
          NGTDLSGAG.PYLDDIDDEMDPEIEEAYEK.CLESEHKRKQ
Retrocopy NGTDLSGAGEPYLDDIDDEMDPEIEEAYEKSCLESEHKRKQ

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	1.32 RPM	24.50 RPM
SRP017611_kidney	1.99 RPM	42.71 RPM
SRP017611_liver	1.00 RPM	39.22 RPM
SRP040447_lung	2.07 RPM	37.88 RPM
SRP040447_skeletal_muscle	2.15 RPM	36.38 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_197 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_197 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Cavia porcellus	ENSCPOG00000002525	2 retrocopies	retro_cpor_133, retro_cpor_197 ,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Ochotona princeps	ENSOPRG00000000386	2 retrocopies	retro_opri_185, retro_opri_469,
Ictidomys tridecemlineatus	ENSSTOG00000011203	1 retrocopy	retro_itri_234,