RetrogeneDB ID: retro_cpor_1153

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_50:702907..704319(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000026543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAP4
• Ensembl ID: ENSCPOG00000022345
• Aliases: None
• Description: Microtubule-associated protein [Source:UniProtKB/TrEMBL;Acc:H0VUD6]

Sequence

>retro_cpor_1153
TCCGGAAATGACATCTCTACCCCACCCAATAAGGAACTCCCACCCAGCCGAGAGACGAGAACCAAGCCTTTGGCCACCAC
TCAACCTGCAAAGACTTCAGCATTGAAAGCCAAAACACAGCTCACTCTTGTCCCTAAGCAGCCAGCTCCTACCACCTCTG
GTGGGGTGAATAAAAAACCCATGAGTCTTGCTTCAGGCTTAGTACCAGCTGCCCCACCCAAACGCCCTGCTGCTGCCACT
GCCAGGACTTCCACCTTTCCTTCAAGAGACCCCAAGCCAAAGCACATTACAGAGGCGAAGGTTCCTGAGAAGCAGGCCCT
ACCATCCAAGCCCGCCTCAGCCCTGGCTTTCCGCTCGGGGCCCAAGAGCATCTCAGCTGCTCTGAAGGTTGCACCAGCTG
CTGCCCCTGCTTCCACAGGGCCAAGCAGTAGAAGTCCTCCAGTGTCAGCATCCAAAAGGCCTGCTGCTCTTAAGATGGAG
GGCAGATCCGCAGACACTAAGAAGATGACGGTGAAGTCCGCACCAGCTGACTTGAGTCGCACCAAGGGTACCCCTACCAG
CTCTGGGAGGAAAGCCACCACTCCTACAGGGGCAGCTCCTCTGGCCACAGCGGCCCCCACTCGGGTCAAGCCTACCCCAC
TTTCCCGGCCCTCTGTGTCTCCTTCCGTGGACAAGAAACCCACTGTGGCCAAGCCCAGCTCTTCTGTCCCCAAGCTGAGC
CACCCAGCCACTGCAGTCCCTGCCCCCGATCTGAAGAACATCCGCTCCAAAGTTGGCTCCACAGAGAATATCAAGCACCA
GCCCGGAGGGGGCCAGGACAAAATAGAGAAAAAAACAGAGGCGTCACCACAGCTCGAAAGCCTGAACCTAATGTAGTCAC
TAAAACAGCTGGTCCTGTTGCGAGCACACAGAAATCGCCTGTTGGGAAAGTCCAGATAGTCTCTAAAAAAGTGAGCTACA
GCCATATTCAGTCCAAGTGTGGTTCCAAGGACAATACTAAGCATGTCCCTGGAGGTGGGAATGTCCAGATCCAGAGCCAG
AAGGTGGACATCTCCAAGGTCTCCTCCAAGTGTGGTTCCAAGGCAAACATCAAGCACAAGCCCGGTGAAGGAGATGTCAA
GATTGAGAGCCAGAAGATGAACTTGAGGGAGAAGGCCCAGGCCAAGGTGGGATCCCGGATAAGGTGGGTCACCTGCCTGC
AGGAGGCACCGTGAAGACTGAGGGATGTGGCAGCAAGGCCCCTCCGTGTCCAGGGCCCCCCAATGGGGAGGAGCTCTGAG
GCTGCGCCTGATGCGAGCCCCCCCCCCCCCCCCCCCGCTCCAGGTGGGGGGCTCAATGGCCTCATCACCCAGTCTGGGGG
GGGGGACCAAAGGGAGGGCCAAACCTTGGACAGCCAGATCCAGGAGAAAAGC

Alignment

ORF - retro_cpor_1153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.71 %
• Parental protein coverage: 95.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TGNDISTPPNKELPPSPEKRTKPLATTQPAKTSASKAKTQLTPVPKQPAPTTSGGSNKKPMSLASGLVPA
          .GNDISTPPNKELPPS.E.RTKPLATTQPAKTSA.KAKTQLT.VPKQPAPTTSGG.NKKPMSLASGLVPA
Retrocopy SGNDISTPPNKELPPSRETRTKPLATTQPAKTSALKAKTQLTLVPKQPAPTTSGGVNKKPMSLASGLVPA

Parental  APPKRPAAATARTSTFPSRDTNIQHITEAKVPEKQALPSKHASALAFRSGPKSISTAPKVASAAAPASTG
          APPKRPAAATARTSTFPSRD....HITEAKVPEKQALPSK.ASALAFRSGPKSIS.A.KVA.AAAPASTG
Retrocopy APPKRPAAATARTSTFPSRDPKPKHITEAKVPEKQALPSKPASALAFRSGPKSISAALKVAPAAAPASTG

Parental  PSSRSPPVSAPKRPAALKTEGRPADTKKMTVKSAPADLSRTKGTPTSSGRKATTPTGAAPLATVAPTRVK
          PSSRSPPVSA.KRPAALK.EGR.ADTKKMTVKSAPADLSRTKGTPTSSGRKATTPTGAAPLAT.APTRVK
Retrocopy PSSRSPPVSASKRPAALKMEGRSADTKKMTVKSAPADLSRTKGTPTSSGRKATTPTGAAPLATAAPTRVK

Parental  PTPLSRPSVSPSVDKKPTAAKPSSSVPKLSRPATAAPAPDLKNIRSKVGSTENIKHQPGGGRAKIEKKTE
          PTPLSRPSVSPSVDKKPT.AKPSSSVPKLS.PATA.PAPDLKNIRSKVGSTENIKHQPGGG..KIEKKTE
Retrocopy PTPLSRPSVSPSVDKKPTVAKPSSSVPKLSHPATAVPAPDLKNIRSKVGSTENIKHQPGGGQDKIEKKTE

Parental  AAP-TARKPEPNAVTKTAGPIASTQKSPAGKVQIVSKKVSYSHIQSKCGSKDNIKHVPGGGNVQIQSQKV
          A.P.TARKPEPN.VTKTAGP.ASTQKSP.GKVQIVSKKVSYSHIQSKCGSKDN.KHVPGGGNVQIQSQKV
Retrocopy ASP<TARKPEPNVVTKTAGPVASTQKSPVGKVQIVSKKVSYSHIQSKCGSKDNTKHVPGGGNVQIQSQKV

Parental  DISKVSSKCGSKANIKHKPGGGDVKIESQKLNFKEKAQAKVGSL-DNVGHLPAGGTVKTEGGGSEAPPCP
          DISKVSSKCGSKANIKHKPG.GDVKIESQK.N..EKAQAKVGS..D.VGHLPAGGTVKTEG.GS.APPCP
Retrocopy DISKVSSKCGSKANIKHKPGEGDVKIESQKMNLREKAQAKVGSR<DKVGHLPAGGTVKTEGCGSKAPPCP

Parental  GP-PIGEEP-AASEAAPDAGAPAPAGGLSGLITLSGGGDQREAQTLDSQIQETS
          GP.P.G....AA..A........P.GGL.GLIT.S....QRE.QTLDSQIQE.S
Retrocopy GP>PMGRSSEAAPDAXXXXXXXXPGGGLNGLITQSXXXXQREGQTLDSQIQEKS

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	2.01 RPM	96.28 RPM
SRP017611_kidney	1.88 RPM	67.00 RPM
SRP017611_liver	1.00 RPM	30.51 RPM
SRP040447_lung	1.03 RPM	123.13 RPM
SRP040447_skeletal_muscle	1.43 RPM	143.07 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1153 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1153 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022345	1 retrocopy	retro_cpor_1153 ,