RetrogeneDB ID: retro_cpor_817

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:26499591..26500715(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000020847
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TINF2
• Ensembl ID: ENSCPOG00000014800
• Aliases: None
• Description: None

Sequence

>retro_cpor_817
CTTGGCCGCCCCAAGGGGGCCGGTCCAGCCACTGGGCGCTTTGTGGCCGCAGCCAGCTTGCAAGTGGTGCGCGAATGCTG
CGGGGAGCATTTCCCTGAGTCCTCCAGCTTCTGAGCTCCCTCTAGGCTGCCGCCCCGGCTTGGTTCGCTACCGGCACCAT
GAGCGCTTGTATATGGGCCTACAGGCCAAGATGGTGGTGGAGATGATCTAGGAGGGCGGCCTTGGCCTCAGGTTCTAAGT
GTCCTGAAATTCCCACAGTCTGGACTTGTACCGCGGGACCCTAAAGCTACAGAGTGGGATCTGAAGATTTTGGAGGCACG
GGAGACCTTTTGCCAGCAGGTGAAGCAACTGTCAGAGGCCCCCGTGAATTTGGCCTCAAAGCTACAGGAGCTTGAAGAAG
AATATGGGGAACCCTTTATGACCGCCATGGAGAAGCTGTTTTTTGAATATTTGTGTCAGCTAGAGAGAGCATTGCCTACC
ATACAGGTACAGCAGCTTCAAGATGTGCTGAGTTGGATGCAGCCTGAAGTTCCTGTCCCCTCTTCTCCTGCCTTGAGCCA
GTATGCTGTGGACATGGGGTGGCCACTTCCAGAGCACTTTGTTTCTAATTCAGTGAACTTGACTGAGCCTGTGGGACAGA
ATCCTCCTACGCAGTCTAGACCAGCTCTCCACAGTCCTCTGCCAAAAGCCAAGCTGAGCCCTGGGGGACCAGCTTCAAAG
AAGCATCAAGAATCTTTTGCTGGCCATCACTTCAATCTGGCCCCACTAGGTCGGCGAAGACGCCAGTCCCGATGGACATC
TGCGAGGGGCGGCTACAAAGAATGCCCCACACTCATGCTGTTGCCCTTTAGGAATCTGGACCCACCAACCCAAGTCATAG
CTCAACCTGAGGGCAGGGAAGAGCATGGGATGCACACAGCAGACACAGCAGGTGTGGGCACAAAAGCAGCCATCACCAGC
AAGTCAAAGAGTCCATATCAAATTCTGGGGGAAAGGCTCTGAAGGAAAACCCACCTGCCTTGTCTGCCTCAGGGGAAATT
GAGAATTGCTTGGATTGTTACTTGGAACCCCTGAGACTACCCTTATCACCTCCAGAGGCCAAGAAGCCAGCACGTTGTCC
ATCT

Alignment

ORF - retro_cpor_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 84.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAPKGAGPATWRIAAAASWQVVRERYVEHFPR-VLQFLRSLRAAAP-GLVRYRHHERLCMGLQAKMVVE
          ...PKGAGPAT.R..AAAS.QVVRE...EHFP..VLQ.L.SL.AAAP.GLVRYRHHERL.MGLQAKMVVE
Retrocopy LGRPKGAGPATGRFVAAASLQVVRECCGEHFPE<VLQLLSSL*AAAP<GLVRYRHHERLYMGLQAKMVVE

Parental  MI-VRGRPWPQVLSVLNRHFPESGLIPRDPKAKEQDLKILEARETFCQQVKQLSEAPVNLASTLQQELEE
          MI...GRPWPQVLSVL...FP.SGL.PRDPKA.E.DLKILEARETFCQQVKQLSEAPVNLAS.LQ.ELEE
Retrocopy MI<LGGRPWPQVLSVLK--FPQSGLVPRDPKATEWDLKILEARETFCQQVKQLSEAPVNLASKLQ-ELEE

Parental  EYGEAFMTAMEKLFFEYLCQLERALPTIQAQQLQDVLSWMQPEVPVPSSLALSQYAVDMGWPLPEHFVSN
          EYGE.FMTAMEKLFFEYLCQLERALPTIQ.QQLQDVLSWMQPEVPVPSS.ALSQYAVDMGWPLPEHFVSN
Retrocopy EYGEPFMTAMEKLFFEYLCQLERALPTIQVQQLQDVLSWMQPEVPVPSSPALSQYAVDMGWPLPEHFVSN

Parental  SVNLTEPVGQNPPTQSRPALHSPLPKAKLSPGGPASKKHRESFAGHHFNLAPLGRRRCQSRWTSARGSYK
          SVNLTEPVGQNPPTQSRPALHSPLPKAKLSPGGPASKKH.ESFAGHHFNLAPLGRRR.QSRWTSARG.YK
Retrocopy SVNLTEPVGQNPPTQSRPALHSPLPKAKLSPGGPASKKHQESFAGHHFNLAPLGRRRRQSRWTSARGGYK

Parental  ERPTVMLLPFRNLDPPSQVIAQPEGREEHGMHTADTAGVGTKAAITSKSKSPSQIL-GGKALKENPPALS
          E.PT.MLLPFRNLDPP.QVIAQPEGREEHGMHTADTAGVGTKAAITSKSKSP.QIL.GGKALKENPPALS
Retrocopy ECPTLMLLPFRNLDPPTQVIAQPEGREEHGMHTADTAGVGTKAAITSKSKSPYQIL<GGKALKENPPALS

Parental  ASGEMENCLGCYLEPLRLPLSPSEAKKPAHCPS
          ASGE.ENCL.CYLEPLRLPLSP.EAKKPA.CPS
Retrocopy ASGEIENCLDCYLEPLRLPLSPPEAKKPARCPS

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	0.12 RPM	15.30 RPM
SRP017611_kidney	0.00 RPM	16.12 RPM
SRP017611_liver	0.04 RPM	9.58 RPM
SRP040447_lung	0.00 RPM	16.54 RPM
SRP040447_skeletal_muscle	0.01 RPM	4.54 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_817 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_817 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	ENSCPOG00000014800	1 retrocopy	retro_cpor_817 ,