RetrogeneDB ID: retro_cpor_1235

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:10560119..10560989(+)
• Located in intron of: ENSCPOG00000012428

Retrocopy information

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

Parental gene information

• Parental gene symbol: KDELC2
• Ensembl ID: ENSCPOG00000005942
• Aliases: None
• Description: None

Sequence

>retro_cpor_1235
AGCCTGGTGTGGGGCCCGGGCTGCAGGTGGCCACTGGCCTTCACAGCAGGTATTTTTACCTGCTGTGGTCAGTACGCAGA
GCCAGAGCTTCCCTGGCTCACTGGACTCCCAGGTCAAACACTATTCAAAATAGTAGTCAAACCTCTTTCACCTAAAGGAG
TAGCCTGGATTCACGTCCCTAAACTTTTGGACAGGAATTGCAGAACATTTTTGGTGTGATATAGAATGTATGACACCATC
AACAAAGGGCTGAAGATCGAGGTCCTTTATACAGTGAACATGGGGCACAGTCTCTCTATATTCTAAAAGGACCTGTGGAC
CATGAGCACGGCTAGTGTCCAGCAGAGGATCCTCAGATGTGGCAGAGAACTCTTTCTTGTATAACCAACAAGCCACAGAT
GAAAGAAGACTTTGACTTTTCCCCCATCATCGATCCCCAGCAGATGGTAAATGAAGCTCCTCAAAGCTTTGAGGATGAGA
GGTATGCGGTTGTTCACTACATGTTTCCAATAACCACATTTACTTGAGATCTGTAGGGAAACACACAACCTTCAGGATGT
TCTCTGATGAGACTTTGCTGTCACTGGCAAGAAAGATTCATCTCCTAGATTTGAAATTTTATATTAATCTTGGAGATTGG
CCCTCAGGGCCTTGAAAAGTTAATGAAACCCCAGGCCCTATACATATCATTTCCTTGTGTGGTTCACTGGATTCAAGAGA
TGTTACCCTTCCAACATATAGTATCACCTACACCAGGCTTGAAACAATGAGAGGTATTACACATTACCTTCTCTCTATTC
AGTAAAATATAGGGCCTCTCCGGATTAACAAATAACAGAATGATTTCTCAGGGGTAGTGATAGAAAGAAA

Alignment

ORF - retro_cpor_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.81 %
• Parental protein coverage: 57.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SLVWGP-GLRAAVVLPVR-YFYLQAVSAQGQNLTR-SPPGQTVFKVVVKPLSSKEVARIHVPAPLDRNDG
          SLVWGP.GL..A..L..R....L..V......L.....PGQT.FK.VVKPLS.K.VA.IHVP..LDRN..
Retrocopy SLVWGP<GLQVATGLHSRYFYLLWSVRRARASLAH>GLPGQTLFKIVVKPLSPKGVAWIHVPKLLDRNCR

Parental  TFLVRYRMYDTVNKGLKIDVLYG-DEHVAQSPYILKGPVYHEYCECPEEDPQAWQEALSCPTWEPQIEED
          TFLV.YRMYDT.NKGLKI.VLY...EH.AQS.YILKGPV.HE...CP.EDPQ.WQ..LSC.T..PQ..ED
Retrocopy TFLV*YRMYDTINKGLKIEVLYT<SEHGAQSLYILKGPVDHEHG*CPAEDPQMWQRTLSCITNKPQMKED

Parental  FASFPTINLQQMLSEVPKRFGDERGAIVHYT-ILNNHIYRRSLGKYTDFKMFSDEILLSLARKVRLPDLE
          F...P.I..QQM..E.P..F.DER.A.VHY....NNHIY.RS.GK.T.F.MFSDE.LLSLARK..L.DL.
Retrocopy FDFSPIIDPQQMVNEAPQSFEDERYAVVHYM<VSNNHIYLRSVGKHTTFRMFSDETLLSLARKIHLLDLK

Parental  FYINLGDWPLEHRKINETPSPVPVISWCGSLDSRDVILPTYDVTHSTLEAMRGVTNDLLSIQGNTGPSWI
          FYINLGDWP....K.NETP.P...IS.CGSLDSRDV.LPTY..T...LE.MRG.T..LLSIQ.N.GP..I
Retrocopy FYINLGDWPSGP*KVNETPGPIHIISLCGSLDSRDVTLPTYSITYTRLETMRGITHYLLSIQ*NIGPLRI

Parental  NKTEKA-FFRGRDSRE
          NK.....F.RG.D...
Retrocopy NK*QND<FLRGSDRKK

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	0.17 RPM	8.11 RPM
SRP017611_kidney	0.00 RPM	5.02 RPM
SRP017611_liver	0.00 RPM	3.22 RPM
SRP040447_lung	0.00 RPM	13.11 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.92 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1235 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1235 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	ENSCPOG00000005942	1 retrocopy	retro_cpor_1235 ,