RetrogeneDB ID: retro_cpor_331

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_129:1561816..1562580(+)
• Located in intron of: ENSCPOG00000015169

Retrocopy information

• Ensembl ID: ENSCPOG00000023007
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BZW1
• Ensembl ID: ENSCPOG00000010449
• Aliases: None
• Description: None

Sequence

>retro_cpor_331
ATGCTGACTGGGATGCTCAACACATCCATCTTCAATAGCCTCTACGATGAGAATCTGGTGAAAGAAGGAAGTCAGCCGCG
TTCACTGTGAAGCTCTTCAAGTCCTGGATCAATGAGAAGGACATCAGTGTGGTGGCCGCGAGCCTTCACAAAGTCAGCAC
GGATAACAGGCTGCGGAAACTTTTTCCTGCCAATAAGCAGAGTGTGGAACACTTCACGGAGGCGAGCCTGAAGGAGCTGT
CCCAGTCCGTCCGGAACCGGTGGACCATCAGTACCTGGAAGGAGCTCCAGAAGGAGCTTCAGGAGCAGATGTCCTGTGGC
GACTCTTTCAAGGACATAATTATATATGTCAAGGAGGAGATGAAAAAGAACAACATCGCAGAACCAGTTGTCACTGGGAT
CGTCTGTTTCAGTGTGATGAGCATGGTGCAGTGCAGCAAAAAAAGAGGAGCTCGTAGCACAACAGGCCATCAAACACTTG
AAGCAATACAGCCCTCGGCTCACTGCCTTCACCACGCAGGGTCACTCGGAGCTGACTCTGTTGCTGAAGATTCAGGAGTA
TTGCTATGACAACATGCACTTCATGAAAGCCTTCCAGAAAATAGTGGTGGTGTTCTACAAAGATGAGGTCCTGATCGAGG
AGCCCATTCTGAAGTGGTACAAGGATGCACACATGGTCAAAAGGAAGAGCATCTTCCTGGAGCAGATGAAGAAGTTCATG
GAGTGGCTAAGAATGCGTCTGAGTCTGAAGTCGAAGACAGGGAC

Alignment

ORF - retro_cpor_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.74 %
• Parental protein coverage: 61.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LANGTLNASILNSLYNENLVKEGV-SAAFAVKLFKSWINEKDINAVAASLRKVSMDNRLMELFPANKQSV
          ...G.LN.SI.NSLY.ENLVKEG..SAAF.VKLFKSWINEKDI..VAASL.KVS.DNRL..LFPANKQSV
Retrocopy MLTGMLNTSIFNSLYDENLVKEGS<SAAFTVKLFKSWINEKDISVVAASLHKVSTDNRLRKLFPANKQSV

Parental  EHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMKKNNIPEPVVIGIV
          E.....FTEA.LKELS..VRN..TI...KELQKELQEQMS.GD.FKDII.YVKEEMKKNNI.EPVV.GIV
Retrocopy E----HFTEASLKELSQSVRNRWTISTWKELQKELQEQMSCGDSFKDIIIYVKEEMKKNNIAEPVVTGIV

Parental  WSSVMSTVEWNKK-EELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIHFMKAFQKIVVL
          ..SVMS.V...KK.EELVA.QAIKHLKQYSP.L.AFTTQG.SELTLLLKIQEYCYDN.HFMKAFQKIVV.
Retrocopy CFSVMSMVQCSKK>EELVAQQAIKHLKQYSPRLTAFTTQGHSELTLLLKIQEYCYDNMHFMKAFQKIVVV

Parental  FYKAEVLSEEPILKWYKDAHMAKGKSVFLEQMKKFVEWL-KNAEEESESEAEDGD
          FYK.EVL.EEPILKWYKDAHM.K.KS.FLEQMKKF.EWL.KNA...SESE.ED.D
Retrocopy FYKDEVLIEEPILKWYKDAHMVKRKSIFLEQMKKFMEWL<KNA---SESEVEDRD

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	0.52 RPM	80.81 RPM
SRP017611_kidney	0.31 RPM	109.40 RPM
SRP017611_liver	0.17 RPM	66.90 RPM
SRP040447_lung	0.66 RPM	131.43 RPM
SRP040447_skeletal_muscle	0.12 RPM	50.91 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_331 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_331 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011878	1 retrocopy	retro_cfam_2150,
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus	ENSCPOG00000010449	1 retrocopy	retro_cpor_331 ,
Homo sapiens	ENSG00000082153	2 retrocopies	retro_hsap_2832, retro_hsap_2881,
Gorilla gorilla	ENSGGOG00000016296	1 retrocopy	retro_ggor_1997,
Mustela putorius furo	ENSMPUG00000012344	1 retrocopy	retro_mputfur_1174,
Mus musculus	ENSMUSG00000051223	3 retrocopies	retro_mmus_2499, retro_mmus_751, retro_mmus_990,
Nomascus leucogenys	ENSNLEG00000006929	1 retrocopy	retro_nleu_621,
Pan troglodytes	ENSPTRG00000012791	1 retrocopy	retro_ptro_1949,