RetrogeneDB ID: retro_cpor_1372

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_74:3955639..3957079(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AA1
• Ensembl ID: ENSCPOG00000002015
• Aliases: None
• Description: None

Sequence

>retro_cpor_1372
GATGACAAACCTGAAATAGAAGATGTTGGTTCTGATGAAGAAGAGGAAGAAAAGAAGGAGGGTGACAAGAAGAAGAAAAA
GAAGATTAAGGAGAAGTATATTGATCAAGAAGAGCTGAACAAAACGAAGCCTATTTGGACCAGAAACCCTGATGATATTA
CTAACGAGGAGTATGGGGAGTTCTACAAAAGCTTGACCAATGATTGGGAGGATCATTTGGCAGTGAAGTATTTTTCCGTG
GAAGGGCAGTTGGAATTCAGGGCTCTTCTTTTTGTTCCACTATGAGCTTCTTTTGACCTATTTGAAAACAGAAAGAAGAA
TAACATTAAGTTGTATGTGCACAGAGTTTTCATCATGGATAACTGTGAGGAACTGATCCCCGAGTACCTGAATTTCTTTA
GAGGGGTGGTGGACTCCGAGGATCTCCCTCTAAATATTTCCAGAGAAATGTTGCAGCAAAGCAAGATCTTGAAAGTCATC
AGAAAAAATTTGGTCAAAAAATGCTTAGAATTGTTTATTGAACTGGTAGAAGATAAGGAGAACTACAAAAAGTTCTATGA
GCAGTTTTCTAAGAATATAAAGCTTGGAATACATGAAGACTCTCAGAATCGGAAGAAGCTCTCAGAACTGTTATGCTACT
ACACATCTGCTTCTGGAGATGAGATGGTTTCTCTCAAGGACTACTGCACTAGGATGAAGGCGAACCAGAAACACATCTAT
TACATCACATGTGAAACCAAAGACCAGGTAGCTAACTCAGCCTTTGTGGAATGTCTTCGAAAGCATAGCTTAGAAGTGAT
CTATATGATCGAGCCCATCGATGAGTACTGTGTCCAGCAGCTGAAAGAATTTGAGGGGAAAACTTTAGTGTCTGTTACCA
AAGAGGGCTTGGAACTTCCAGAAGATGAAGAAGAGAAAAAGAAACAGGAGGAGAAAAAGACAAAGTTTGAAAACCTCTGC
AAGATCATGAAAAATATTTTGGAGAAAAAGGTCAAAAAGGTAGTTGTATCAAACCGATTGGTGACATCCCCATGCTGTAT
TGTCACCAGTACATATGGCTGGACAGCAAACATGGAGAGAATCATGAAAGCCCAAGCCCTAAGAGACAACTCCATGATGG
GGTACATGGCAGCCAAGAAGCACCTGGAGATAAACCCTGACCACTCAATCATGGAGACCTTGAGGCAGAAGGCCAAGGCT
GATAAGAATGACAAGTCCGTGAAGGATCTGGTCATCTTGCTGTATGAAACTGCCCTGCTATCCTCTGGCTTCAGTCTGGA
AGAGCCTCAGACACATGCAAACAGAATCTACAGGATGCTCAAGCTGGGGCTAGGTATTGATGAGGACGACCCCACTGCTG
ATGACACCACTGCTGCTGTCAATGAAGAGATGCTGCCCCTTGAAGGAGATGATGACACATCACGCATGGAAGAAGTTGAC

Alignment

ORF - retro_cpor_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 65.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDKPEIEDVGSDEEEEEKKDGDKKKKKKIKEKYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWE
          DDKPEIEDVGSD....................YIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWE
Retrocopy DDKPEIEDVGSDXXXXXXXXXXXXXXXXXXXXYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWE

Parental  DHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDS
          DHLAVK.FSVEGQLEFRALLFVP..A.FDLFENRKK.NNIKLYV.RVFIMDNCEELIPEYLNF.RGVVDS
Retrocopy DHLAVKYFSVEGQLEFRALLFVPL*ASFDLFENRKK-NNIKLYVHRVFIMDNCEELIPEYLNFFRGVVDS

Parental  EDLPLNISREMLQQSKILKVIRKNLVKKCLELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSE
          EDLPLNISREMLQQSKILKVIRKNLVKKCLELF.EL.EDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSE
Retrocopy EDLPLNISREMLQQSKILKVIRKNLVKKCLELFIELVEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSE

Parental  LLRYYTSASGDEMVSLKDYCTRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQ
          LL.YYTSASGDEMVSLKDYCTRMK.NQKHIYYIT.ETKDQVANSAFVE.LRKH.LEVIYMIEPIDEYCVQ
Retrocopy LLCYYTSASGDEMVSLKDYCTRMKANQKHIYYITCETKDQVANSAFVECLRKHSLEVIYMIEPIDEYCVQ

Parental  QLKEFEGKTLVSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVT
          QLKEFEGKTLVSVTKEGLEL................FENLCKIMK.ILEKKV.KVVVSNRLVTSPCCIVT
Retrocopy QLKEFEGKTLVSVTKEGLELXXXXXXXXXXXXXXXXFENLCKIMKNILEKKVKKVVVSNRLVTSPCCIVT

Parental  STYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKDLVILLYETAL
          STYGWTANMERIMKAQALRDNS.MGYMAAKKHLEINPDHSI.ETLRQKA.ADKNDKSVKDLVILLYETAL
Retrocopy STYGWTANMERIMKAQALRDNSMMGYMAAKKHLEINPDHSIMETLRQKAKADKNDKSVKDLVILLYETAL

Parental  LSSGFSLEDPQTHANRIYRMIKLGLGIDEDDPTADDTTAAVNEEMPPLEGDDDTSRMEEVD
          LSSGFSLE.PQTHANRIYRM.KLGLGIDEDDPTADDTTAAVNEEM.PLEGDDDTSRMEEVD
Retrocopy LSSGFSLEEPQTHANRIYRMLKLGLGIDEDDPTADDTTAAVNEEMLPLEGDDDTSRMEEVD

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	0.81 RPM	1064.63 RPM
SRP017611_kidney	0.73 RPM	973.07 RPM
SRP017611_liver	0.57 RPM	770.64 RPM
SRP040447_lung	0.63 RPM	800.16 RPM
SRP040447_skeletal_muscle	0.26 RPM	427.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1372 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1372 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 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372 ,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860,