RetrogeneDB ID: retro_cpor_1491

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:55654785..55655794(+)
• Located in intron of: ENSCPOG00000015520

Retrocopy information

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

Parental gene information

• Parental gene symbol: KANSL2
• Ensembl ID: ENSCPOG00000005760
• Aliases: None
• Description: None

Sequence

>retro_cpor_1491
ATGAACAGGATTCAGATTCATATCTTGCCAAACAACCAGAGCAGAATTACAACAGTTCCCAGGTCACAGGAGCCCTTGTG
TTCATTCAGTCATCGCCCATGCTCTCAGTCCCTCATCTGGAAGGACAGGAATCTGCATTCAGCGTATCCTCGAAGACAAA
AATACACCCTTCAAGCAGAGTAGTTATATATCCACAAAGAATGGAAAAAGATGTCCCAGTGCTGCCTTAAAGCCGGAGAA
GAAAGATGGTGTGTCCTTCTGTGCTGAACACGCTCATAGGAATGCCTTAGCACTTCATGCTCAAATGAATAAGACCAGCC
CAGGGCCTATGGGTGAAACACTGCTGTGCCAGCTGAGTTCACATGCTGAGATGCAGGTGGGATCTCAGACTCCAGAAAGT
ATCCATAGTGAAGCCAGTCAAATACTGCATGAAGACAGCTGGAGTGATGGGGACAAGGAACCCACTACTGGGAATCAGAC
ATGGAAAGGTGACCCTGACAGCGAAGCTGATAGCATAGACAGTGATCAAGAAGATCCCCTAAAACATGCAAGCGTCTACA
CAGCAGAAGAAGTGGCCCTGATTATGTGTGAGAAATTAATTCGCTTGCAGTCTTTATACATTGATCAGTTTAAACAACTT
CAGCACCTGCCCGAGAAGAAGTGCCGGTACTTACATAACCGCAAAGTGGAACATGAGGCTTTAGGCAGCGGTCTCCTGAC
CAGCCCAGAGGGACACTTAGTAAAGAAAGAGAGATTTTAAAGTGATTAAAATGTCTCCAGTGTATTGCCAGCACTATGGA
GTGGAGGAAGCCTTACTAAACATGCAACTGAAGGAAGGCAGAACGCTGGCACAGATGGTGGTGCCCAGGAAGCCCATACC
ACTCATTCCATTCAGTGGTGCTTGGCCTTCATGGATACTGTTCGTTGTTCTAATCAGTCTCTTCCAATGAGCAGATAGTG
CTGCACCCAGACTTGTCAGGATATGAATCAAGTGCTCTTCAAACACTGC

Alignment

ORF - retro_cpor_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.43 %
• Parental protein coverage: 68.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNRIRIHVLPTNRGRITPVPRSQEPLSCSFTHRPCSQ-PRLEGQEFCIKHILEDKNAPFKQCSYISTKNG
          MNRI.IH.LP.N..RIT.VPRSQEPL.CSF.HRPCSQ.P.......CI..ILEDKN.PFKQ.SYISTKNG
Retrocopy MNRIQIHILPNNQSRITTVPRSQEPL-CSFSHRPCSQ>PSSGRTGICIQRILEDKNTPFKQSSYISTKNG

Parental  KRCPSAAPKPEKKDSVSFCAEHARRNALAVHAQMKKTSPGPMGETLLCQLSSYAKTEVGSQTPESIRSEA
          KRCPSAA.KPEKKD.VSFCAEHA.RNALA.HAQM.KTSPGPMGETLLCQLSS.A...VGSQTPESI.SEA
Retrocopy KRCPSAALKPEKKDGVSFCAEHAHRNALALHAQMNKTSPGPMGETLLCQLSSHAEMQVGSQTPESIHSEA

Parental  SRILDEDSWSDGDQEPITVDQTWRGDPDSEADSIDSDQEDPLKHAGVYTAEEVALIMREKLIRLQSLYID
          S.IL.EDSWSDGD.EP.T..QTW.GDPDSEADSIDSDQEDPLKHA.VYTAEEVALIM.EKLIRLQSLYID
Retrocopy SQILHEDSWSDGDKEPTTGNQTWKGDPDSEADSIDSDQEDPLKHASVYTAEEVALIMCEKLIRLQSLYID

Parental  QFKRLQHLLKEKKRRYLHNRKVEHEALGSSLLTGPE-GLLAKERENLKRLKCLR-RYRQRYGV-EALLHR
          QFK.LQH.L.EKK.RYLHNRKVEHEALGS.LLT.PE.G.L.KERE.LK.LKCL...Y.Q.YGV.EALL..
Retrocopy QFKQLQH-LPEKKCRYLHNRKVEHEALGSGLLTSPE<GTLSKEREILK*LKCLQ<VYCQHYGVEEALLNM

Parental  QLKERRMLA-TDGGAQQAHTTRSSQRCLAFVDDVRCSNQSLPMTRHCLTHICQDTNQVLFKCC
          QLKE.R.LA.TDGGAQ.AHTT.S.Q.CLAF.D.VRCSNQSLPM.R.C.T..CQD.NQVLFK.C
Retrocopy QLKEGRTLA<TDGGAQEAHTTHSIQWCLAFMDTVRCSNQSLPMSR*CCTQTCQDMNQVLFKHC

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	19.21 RPM
SRP017611_kidney	0.00 RPM	22.72 RPM
SRP017611_liver	0.00 RPM	10.40 RPM
SRP040447_lung	0.00 RPM	29.33 RPM
SRP040447_skeletal_muscle	0.01 RPM	19.81 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1491 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1491 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005760	1 retrocopy	retro_cpor_1491 ,
Dipodomys ordii	ENSDORG00000001180	1 retrocopy	retro_dord_474,
Mus musculus	ENSMUSG00000022992	2 retrocopies	retro_mmus_2944, retro_mmus_3134,
Rattus norvegicus	ENSRNOG00000010904	3 retrocopies	retro_rnor_1071, retro_rnor_2831, retro_rnor_792,
Tupaia belangeri	ENSTBEG00000016536	1 retrocopy	retro_tbel_1374,