RetrogeneDB ID: retro_cpor_133

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:46467302..46468465(+)
• 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_133
GAACAAACGAGGCCCCTGAGAGCTCCACCTAGCTCACAGGATAAAACCCCATAGCAGAACTCAGAGTCAGCAATGGCTAA
GCCCCAGGAAGTTGTGGCTCCTGTGTTAATGTCTAAGCTGTCTGCCAATGCCCCCGAATTTTACCCATCAGGTTATTCTG
CTTATACAGAATCCTATGAAGATAGTTGTGAGGATTATCCCACTCTATCAGACTATGTTCAAGAGTTTTTGAATCATCTT
ACAGAGCAACCTGGCAGTTTTGAAACTGAAATTGAACAATTTGCAGAGACCCTGATTAGCTGGGTTACAACTGATGATGC
TTTGCAAGAACTTGTGGAACTCATCTACCAACAGGCCACATCTATCCCAAATTTCTCTTACATGGGAGCTCGCCTGTGTA
ATTACCTGTCCCATCATCTGACAATTAGTCCACAGAGTGGCAACTTCTGCCAATTGCTTCTTCAAAGATGTCGGACTGAA
TATGAAGTTAAAGATCAAGCTGAGAAAGGAGATGAAGTGACTCGAAAGCGATTTCATGCATTTGTACTCTTTCTGGGAGA
ACTTTATCTTAACCTGGAGATCAAGGGAACAAATGGGCAGGTTACGAGAGCAGATATTCTTCAAATTGGTCTGCGTGAAT
TGCTGAATGCCCTCTTCTCTAATCCAATGGATGACAACTTAATTTGTGCAGTAAAATTATTAAAGTTGACAGGATCAGTT
TTGGAAGATGCTTGGAAAGAAAAATTAAAGACTGATATGGAAGAAATTATTCAAAGAATTGAAAATGTTGTCCTAGATGC
AAATTACAGCAGAGATGTAAAATAGAGGCTCTTGAAGCTTGTAGAACTTCGGTCAAGTAACTGGGGCAGAGTACATGCAA
CTTCAACGTACAGAGAAGCAACACCTGAAAATGATCCTAACTACTTTATGAATGAACCAACATTTTATACATCTGATGGT
GTTCCTTTCACTGCAGCAGATCCAGATTACCAAGAGAAGTATCAAGAGTTACTTGAAAGAGAGGCCTTTTTTCCAGATTA
TGAAGAAAATGGAACAGATTATCAGGTGATCCATACTTGGATGATATTGATGATGAGATGGACCCAGAAATTGAAGAAGC
TTATGAAAAGTTTTGTTTGGAATCAGAGCATAAGCGAAAACAG

Alignment

ORF - retro_cpor_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.14 %
• Parental protein coverage: 92.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQTRPLRAPPSSQDKTPQQNSESAMAKPQVVVAPVLMSKLSANAPEFYPSGYSAYTESYEDGCEDYPTLS
          EQTRPLRAPPSSQDKTP.QNSESAMAKPQ.VVAPVLMSKLSANAPEFYPSGYSAYTESYED.CEDYPTLS
Retrocopy EQTRPLRAPPSSQDKTP*QNSESAMAKPQEVVAPVLMSKLSANAPEFYPSGYSAYTESYEDSCEDYPTLS

Parental  DYVQEFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHL
          DYVQEFLNHLTEQPGSFETEIEQFAETL..WVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHL
Retrocopy DYVQEFLNHLTEQPGSFETEIEQFAETLISWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHL

Parental  TISPQSGNFRQLLLQRCRIHHKVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVG
          TISPQSGNF.QLLLQRCR....VKDQA.KGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQ.G
Retrocopy TISPQSGNFCQLLLQRCRTEYEVKDQAEKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQIG

Parental  LRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKLKTDMEEIIQRIENVVLDANCSRDVKQMLLKL
          LRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKLKTDMEEIIQRIENVVLDAN.SRDVK..LLKL
Retrocopy LRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKLKTDMEEIIQRIENVVLDANYSRDVK*RLLKL

Parental  VELRSSNWGRVHATSTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEEN
          VELRSSNWGRVHATSTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLERE.FFPDYEEN
Retrocopy VELRSSNWGRVHATSTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREAFFPDYEEN

Parental  GTD-LSGAGDPYLDDIDDEMDPEIEEAYEKFCLESEHKRKQ
          GTD.LSG..DPYLDDIDDEMDPEIEEAYEKFCLESEHKRKQ
Retrocopy GTD<LSG--DPYLDDIDDEMDPEIEEAYEKFCLESEHKRKQ

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	0.92 RPM	24.50 RPM
SRP017611_kidney	2.62 RPM	42.71 RPM
SRP017611_liver	1.78 RPM	39.22 RPM
SRP040447_lung	2.60 RPM	37.88 RPM
SRP040447_skeletal_muscle	3.45 RPM	36.38 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_133 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_133 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.

---

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,