RetrogeneDB ID: retro_cpor_362

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_132:1435400..1436677(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000015204
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LACC1
• Ensembl ID: ENSCPOG00000011253
• Aliases: None
• Description: None

Sequence

>retro_cpor_362
ATGGCAGAAGCAGTTTTCATTGATCTGTTTGGCCTGGAATTGGACTCTCAGGAAAACTGCCATCAGACATTACTGAAGAC
ACTAAATACAGTCCAATACCACCATGCTGGCAAGGCTCAGTTCCTGTGTATAATATGTTGCAGTAACATGAGCTGCGAGT
GGGATAGTGAACATAATAATTGTGAACTGGAAACAAGCAATGAATTTTCAGCCTTCTTGAATGACTTTGAGATTGTTAGT
AATCCAAGCCTGGCTGCCTCTTTGTACACCGTTAAGCAAAAAATTAATGAAAAAAATGTGAGCAGTATTAAGGTGATTGT
ACCGGTACACAGGACAACACTAATGAAAGCTTTTATTGATCAACACTTTACTGAGGTTTACAGTTTTGAGTTTGAAGATT
TACAGGTAAAGGATGGCCCTTTGAAGCAGTCCACTGAAGTGATCGCAGCTCCTGAACTAGAAAAATCCAAGATGAAATAA
AAATGTATTTGAGAAGTCTGCCATCCCTGAATGGAAAATTAACTGTTATTACATCTTCTCTGATCCCAGACATTTTCATA
CATGGATTTACTACAAGAGCAGGTGGGATATCTTACATATCAACTCTTAGCTCATTAAATCTCTTCAGTAGTTCCAAACG
GAGAGATCCCAAAATGGTTGTTCAAGAAAACCTGCGTAGGTTGGCAAGTACTGCAGGATTTAACGCAGAGAAATTTTACC
GAGTAAAGACTGATCACGCCAATGAAGTCTGGATTATGGGGAAAAAAGAGCCTGAATTTTATGATGGAATAACCACAAAT
CAGAAAGGAGTCACAATAGCAGCTCTTGGTGCTGACTGTATACCTACAGTTTTTGCAGATCCTGTTAAAAAAGCATGTGG
AGTTGCTCATTCTGGATGGAAAGGTACTTTGTTAGGTGTTGCTATGGCAACAGTAAAGGCAATGATATCAGAATATGACT
GTCGTTTGGAAGACATTATTGCTGTATTGGGACCTTCAGTAGGACCTTGCTGTTTTACTTTTCCCAAAGAATCAGCAGAT
GCATTTCATAATCTTCATCCTGCATGTGTACGACTGTTTGACTCACCAGATCCCTACATCGACCTCCGTAAAGCTGCTAG
GATTCTTCTAGAACAAGAAAGAATTCTACCACAGAATATTCAGGACCAGAACCAAGATCTCGACCTCTGTACATCCTGCC
ATCCTGAAAATCTTTTCTCCTTCGTGTGAGATGGTCTTAACTTTGGTACACAGATTGGCTTCATATCAATTAGAGAC

Alignment

ORF - retro_cpor_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEAVLIDLFGLELDSQEKCHQTLRKTLNTVRHHHAGKAQFLCIICCSNMSCEWDSEHDNCKLETSNEFS
          MAEAV.IDLFGLELDSQE.CHQTL.KTLNTV..HHAGKAQFLCIICCSNMSCEWDSEH.NC.LETSNEFS
Retrocopy MAEAVFIDLFGLELDSQENCHQTLLKTLNTVQYHHAGKAQFLCIICCSNMSCEWDSEHNNCELETSNEFS

Parental  AFLNDFEIVSNPSMAASLYIVKQKIDEKNVRSIKVIVPVHRTTLMKAFIDQLFTEVYSFEFEDLQVKDGL
          AFLNDFEIVSNPS.AASLY.VKQKI.EKNV.SIKVIVPVHRTTLMKAFIDQ.FTEVYSFEFEDLQVKDG.
Retrocopy AFLNDFEIVSNPSLAASLYTVKQKINEKNVSSIKVIVPVHRTTLMKAFIDQHFTEVYSFEFEDLQVKDGP

Parental  LKQSTEVITAPELE-KIQDEIKMYLRSLPSLNGKLTVITSSLIPDIFIHGFTTRAGGISYIPTLSSLNLF
          LKQSTEVI.APELE.KIQDEIKMYLRSLPSLNGKLTVITSSLIPDIFIHGFTTRAGGISYI.TLSSLNLF
Retrocopy LKQSTEVIAAPELE<KIQDEIKMYLRSLPSLNGKLTVITSSLIPDIFIHGFTTRAGGISYISTLSSLNLF

Parental  SSSKRRDPKMVVQENLRRLASTAGFNAEKFYRVKIDHANEVWIMGKKEPEFYDGITTNQKGVTIAALGAD
          SSSKRRDPKMVVQENLRRLASTAGFNAEKFYRVK.DHANEVWIMGKKEPEFYDGITTNQKGVTIAALGAD
Retrocopy SSSKRRDPKMVVQENLRRLASTAGFNAEKFYRVKTDHANEVWIMGKKEPEFYDGITTNQKGVTIAALGAD

Parental  CIPIVFADPVKKACGVAHSGWKGTLLGVAMATVKAMISEYDCRLEDIIVVLGPSVGPCCFTLPKESADAF
          CIP.VFADPVKKACGVAHSGWKGTLLGVAMATVKAMISEYDCRLEDII.VLGPSVGPCCFT.PKESADAF
Retrocopy CIPTVFADPVKKACGVAHSGWKGTLLGVAMATVKAMISEYDCRLEDIIAVLGPSVGPCCFTFPKESADAF

Parental  HNLHPACVRLFDSPDPYIDLRKATRILLEQGGILPQNIQDQNQDLNLCTSCHPEKFFSFVRDGLNFGTQI
          HNLHPACVRLFDSPDPYIDLRKA.RILLEQ..ILPQNIQDQNQDL.LCTSCHPE..FSFV.DGLNFGTQI
Retrocopy HNLHPACVRLFDSPDPYIDLRKAARILLEQERILPQNIQDQNQDLDLCTSCHPENLFSFV*DGLNFGTQI

Parental  GFISIRD
          GFISIRD
Retrocopy GFISIRD

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	3.22 RPM
SRP017611_kidney	0.10 RPM	10.68 RPM
SRP017611_liver	0.00 RPM	9.88 RPM
SRP040447_lung	0.03 RPM	12.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_362 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_362 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011253	1 retrocopy	retro_cpor_362 ,
Ochotona princeps	ENSOPRG00000013275	1 retrocopy	retro_opri_431,