RetrogeneDB ID: retro_cpor_1174

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:8313972..8314894(-)
• Located in intron of: ENSCPOG00000005288

Retrocopy information

• Ensembl ID: ENSCPOG00000021589
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SERPINB5
• Ensembl ID: ENSCPOG00000013882
• Aliases: None
• Description: None

Sequence

>retro_cpor_1174
GGATTTCAAACAATTACCTTGGATGTAAATAAACTTAGTTCCTTTTACTCTTTGAAACTAATCAAGCGGCTCTATGTAGA
CAAATCTCTGAACCCTTCTACAGAATTCCTCAACTCTACAAAGAGACCATATACGAAAGAATTGGAAACTGTTGATTTCA
AAGATAAACTGGATGAAACGAAAGTTCAGATCAACAACTCCATTAAGGAGCTCACAGATCGCTACTTTGAGAACATTTTA
TCTGACAATAGTGTGAACAACCAGACCAAAATCCTTGTGGTTAATGCTGCCTACTTTGTTGGAAAGTGGATGGAAGAAAT
GTCCCGAATCAGAAACGAAGGAATGCCCTTTCAGAGTCAGCAAGACAGACACCAAACCAGTACAAATGATGAATCTGGAG
GCCACATTTTGTCTGGGGAATATTGATGACATCAACTGTAAAATCATAGAGCTTCCTTTTCAAAACAAGTACCTCAGCAT
GTTCATCCTTCTCCCCAAAGATGTGGATGATGAGTCCACGGGCGTGGAGAAGATTGAAAAACAACTCAATGCAGAAACCC
TGTCACAGTGGACCAATCCCAGCACCATGGCCAATGCCAAAGTCAAACTCTCCCTTCCAAAGTTTAAAGTGGAAAAAATG
GTTGATCCTAAGGCTAGCCTGGAAAACTTAGGGCTGAAAAATTTATTTAATGAAAACACATCTGATTTCTCTGGAATGTC
AGAAACAAAGGGAGTGGCCTTATCAAACGTGATTCACAGAGTGTGCTTAGACATAACTGAAGATGGTGGAGATTCCATAG
AGGTGCCAGGATCCCGGATCCTGCAACATAAGGATGAATTCAATGCTGACCACCCATTTGTTTACTTCATCAGGCACAAC
AAAACGTGAAACATCATTTTCTTTGGCAAGTTCTGTTCTCCT

Alignment

ORF - retro_cpor_1174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 81.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFQTVTSDVNKLSSFYSLKLIKRLYVDKSLNPSTEFLSSTKRPYAKELETVDFKDKLDETKVQINNSIKE
          GFQT.T.DVNKLSSFYSLKLIKRLYVDKSLNPSTEFL.STKRPY.KELETVDFKDKLDETKVQINNSIKE
Retrocopy GFQTITLDVNKLSSFYSLKLIKRLYVDKSLNPSTEFLNSTKRPYTKELETVDFKDKLDETKVQINNSIKE

Parental  LTDGYFENILSDNNVNDQTKILVVNAAYFVGKWM-KKFPESETKECPFRVSKTDTKPVQMMNLEATFCLG
          LTD.YFENILSDN.VN.QTKILVVNAAYFVGKWM.KK.PESETKECPFRVSKTDTKPVQMMNLEATFCLG
Retrocopy LTDRYFENILSDNSVNNQTKILVVNAAYFVGKWM>KKCPESETKECPFRVSKTDTKPVQMMNLEATFCLG

Parental  NIDDINCKIIELPFQNKHLSMLILLPKDVDDESTGLEKIEKQLSAETLSQWTNPSTMANAKVKLSLPKFK
          NIDDINCKIIELPFQNK.LSM.ILLPKDVDDESTG.EKIEKQL.AETLSQWTNPSTMANAKVKLSLPKFK
Retrocopy NIDDINCKIIELPFQNKYLSMFILLPKDVDDESTGVEKIEKQLNAETLSQWTNPSTMANAKVKLSLPKFK

Parental  VEKMVDPKASLENLGLKNLFNENTSDFSGMSETKGVALSNVIHRVCLDITEDGGDSIEVPGSRILQHKDE
          VEKMVDPKASLENLGLKNLFNENTSDFSGMSETKGVALSNVIHRVCLDITEDGGDSIEVPGSRILQHKDE
Retrocopy VEKMVDPKASLENLGLKNLFNENTSDFSGMSETKGVALSNVIHRVCLDITEDGGDSIEVPGSRILQHKDE

Parental  FNADHPFVYFIRHNKTRNIIFFGKFCSP
          FNADHPFVYFIRHNKT.NIIFFGKFCSP
Retrocopy FNADHPFVYFIRHNKT*NIIFFGKFCSP

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	0.12 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.52 RPM
SRP040447_lung	0.10 RPM	0.33 RPM
SRP040447_skeletal_muscle	0.05 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1174 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1174 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013882	1 retrocopy	retro_cpor_1174 ,
Rattus norvegicus	ENSRNOG00000002640	1 retrocopy	retro_rnor_2400,
Ictidomys tridecemlineatus	ENSSTOG00000007438	1 retrocopy	retro_itri_115,