RetrogeneDB ID: retro_cpor_171

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:29303532..29304716(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000021665
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000012382
• Aliases: None
• Description: None

Sequence

>retro_cpor_171
ACAAAAAATAAGGCCTTACAATCAAAAACAGTTCTACCTGTGGTCAAAACCTCTTCTCAGGACGTAAAAAAGAAGTAAGA
CATTATCCCAAAACACATCTGAAAATATAGCCAGGCCTATTTCATTTACTAATATCAAACTGACAGAAAAGTCAAAAACT
GTTGACCACCGAAGACATACGTTAGCAAAAGCCACTGTGGATGGATCAGCTCAGCTCAAAGAAACTGCAGAAGAAAGAAA
AGCTCATCTGAATGAGTGCAGAGCTGGCAAAGGAAGAGTGCTGAAGAGGCCTCCGAACCCAGTCTCTGCCCAGCCCGAGC
CTGAGGGACAAAATGCAAACCCCGCTGGATCATTCTGGACTACTATGGCAGAAGAGGATGAGCAAAGATTAATTTACTGA
CAAAGTGAACAAGATATTTTCTGAATGCCTGAACCTCATTCATGAGGGATACCCCAAAGAAGAAATAATGACCACACTGA
ATGACGTGATTAAAAATATTCCAGATGCTAAAAAATCTTGTTAAATATTGGATATGTCTTATACGTATTGAATCAATCAC
AAGTCCTGTTGAAAACATTATCTCAATCTATGAGAAGGCCGTTCTTGCAGGAGCTCAGCCAATTGAAGAGATGCGACAGA
CAATTGTGGATATTATAACAATGAAGAACCAAGAAAAAAGTAACTGTGAAAAAAATATTGAAGATGCTTGTAAAACCAAG
GAACAAATCCAGGAAGTCAACACTGAGGATACAGGTGTTAATCTAGAGCCAGGAAAACAAGAAATGGAGAATAAACATAG
TAGAAATGTGGTGTTTGAAGGTTGTGAACAACAGCAAGATGACACAAAAATCCAAGTGACAATTTTAAAACCCCTGATGC
AGAAAATAGATCAGGTTGCTTAATTAAATATAACACATCTACTACACCATACTTGCAGAGCATAAAAAAGAAGATGCAAT
TTGATGAAACAAATCCTGCACTTAAAGAGCTAAAGTTTCTAACACCAGTGAGACGTTCTCGACGCCTTCAAGAGAAGACT
TCTAAATTGCCAGACATGTTAAAAGACCATTACCCTTGTGTGTCTTCACTGGAACAGTTGTCAGAGTTAGGAGGTGGAAC
TGATGCTTTTGTATGTCGCCCAAACGTAGCTCTGTGCCCTATGTACTCTGAGACTGATACTTCA

Alignment

ORF - retro_cpor_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 59.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TEKEQLQSETVLGSVKSSSQDVK-RSKTLSQNTSENIARPISFPNIKLTEKSKTVDHRRHTLAKATVDGS
          T....LQS.TVL..VK.SSQDVK.RSKTLSQNTSENIARPISF.NIKLTEKSKTVDHRRHTLAKATVDGS
Retrocopy TKNKALQSKTVLPVVKTSSQDVK>RSKTLSQNTSENIARPISFTNIKLTEKSKTVDHRRHTLAKATVDGS

Parental  AQLKETAKERKAHLNESRAGKGRVLKRPPNPVSAQPEPEGPNANPVGSFWTTMAEEDEQRL-FTDKVNKI
          AQLKETA.ERKAHLNE.RAGKGRVLKRPPNPVSAQPEPEG.NANP.GSFWTTMAEEDEQRL.FTDKVNKI
Retrocopy AQLKETAEERKAHLNECRAGKGRVLKRPPNPVSAQPEPEGQNANPAGSFWTTMAEEDEQRL>FTDKVNKI

Parental  FSECLKLIHEGYPKEEIMTTLNDVIKNIPDAKK-LVKYWICLIRIESITSPVENIISIYEKAILQELRPI
          FSECL.LIHEGYPKEEIMTTLNDVIKNIPDAKK.LVKYWICLIRIESITSPVENIISIYEKA.L....PI
Retrocopy FSECLNLIHEGYPKEEIMTTLNDVIKNIPDAKK>LVKYWICLIRIESITSPVENIISIYEKAVLAGAQPI

Parental  EEMRQTVVDIITMKNQEKSNCGKNIEDACKTKEQIQEVNTEDTGVNLEPGKQEMENKHSRNVVFEGCEQQ
          EEMRQT.VDIITMKNQEKSNC.KNIEDACKTKEQIQEVNTEDTGVNLEPGKQEMENKHSRNVVFEGCEQQ
Retrocopy EEMRQTIVDIITMKNQEKSNCEKNIEDACKTKEQIQEVNTEDTGVNLEPGKQEMENKHSRNVVFEGCEQQ

Parental  QDDTK-NPSDNFKTPDAENRSGCLIKYNISTTPYLQSIKKKMQFDETNPALKELKFLTPVRRSRRLQEKT
          QDDTK.NPSDNFKTPDAENRSGCLIKYN.STTPYLQSIKKKMQFDETNPALKELKFLTPVRRSRRLQEKT
Retrocopy QDDTK<NPSDNFKTPDAENRSGCLIKYNTSTTPYLQSIKKKMQFDETNPALKELKFLTPVRRSRRLQEKT

Parental  SKLPDMLKDHYPCVSSLEQLSELGGETDAFVCRPNVALCPMYSETDTS
          SKLPDMLKDHYPCVSSLEQLSELGG.TDAFVCRPNVALCPMYSETDTS
Retrocopy SKLPDMLKDHYPCVSSLEQLSELGGGTDAFVCRPNVALCPMYSETDTS

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	1.44 RPM
SRP017611_kidney	0.21 RPM	5.34 RPM
SRP017611_liver	0.09 RPM	1.74 RPM
SRP040447_lung	0.08 RPM	3.93 RPM
SRP040447_skeletal_muscle	0.04 RPM	1.39 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_171 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_171 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973,
Cavia porcellus	ENSCPOG00000010435	2 retrocopies	retro_cpor_229, retro_cpor_528,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171 ,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491, retro_ttru_1741,