RetrogeneDB ID: retro_cpor_1391

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:19774237..19774881(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPTG
• Ensembl ID: ENSCPOG00000014046
• Aliases: None
• Description: None

Sequence

>retro_cpor_1391
GTGACCTGGCATTAGCAGCCCTTTGGCTGAGACATCTATATTGGGGTCCTTGGCATCGGCATGAGTGGAAGATCACCAAC
AACACCTTCAGGGTCATGCAGATGAGGGCTGGTGACTCCTGCCATGCCTGAAGCCAGCAGTGCAAGGTGGAGCTTACCTG
TAGGAGGAGCAATAGAGTGGCCCATGTGTCTGAGCCAATCACGTGTGTCTATGTGCTGATGTTGCTAACACCCCTTGCCT
GCCACCCCACTCTCTATTACCCAGCCCTGCTGGGAGCTCTGCAGCACAGGGGCAGGCAGGTGAAGCAGGACCTGTATGGT
GAGCTCATCACCACCCAGGGCCATGAAAAGCTGCAGAGGGAGCTTTTTGAGGACACTGGCTATGTAAAGGCCCCAAGAGA
AAAGAAACCCACACTGCAGGAAGGAGCACCTAGGAGTCTAGGGACTGGGACTCTGTAGAACTACAATCAGGCATGTTCAG
AGCTGTGAGGGGAAACACAGAGTCTCAGCAGTCTTCAAGCCTGTGTGGCAGCCCCACGGGAGGCCCACAGAAACCTCCCA
CACTGAGCACTCAGCCCAACAGTCCCCACAGACATGACTTCAGAGCAACTGTGAGGATCTGGGCTTCTATGGGGACAACT
GATG

Alignment

ORF - retro_cpor_1391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.06 %
• Parental protein coverage: 71.24 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VTQHEQTFRWNAYSGVLGIW-HEWEIANNTFVGMWMRDGDSCRARSRQSKVELTCGKNNRLAHVSEPSTC
          VT.H.Q.F....Y.GVLGI..HEW.I.NNTF..M.MR.GDSC.A.S.Q.KVELTC...NR.AHVSEP.TC
Retrocopy VTWH*QPFG*DIYIGVLGIG<HEWKITNNTFRVMQMRAGDSCHA*SQQCKVELTCRRSNRVAHVSEPITC

Parental  VYALTFETPLVCHPHSLLVYPTLPEALQRRWDQVEQDLADELITLQGYEKLLRELFEDAGYLKAPRENEP
          VY.L...TPL.CHP...L.YP.L..ALQ.R..QV.QDL..ELIT.QG.EKL.RELFED.GY.KAPRE..P
Retrocopy VYVLMLLTPLACHP--TLYYPALLGALQHRGRQVKQDLYGELITTQGHEKLQRELFEDTGYVKAPREKKP

Parental  TQQEGTARGLGTETLENCNKARSELTEEIQRLTSL-LNLHGIP-HERPTETSHTEHLAQQS-PTDVTSEQ
          T.QEG..R.LGT.TL.N.N.A.SEL..E.Q.L.SL...L.G.P.H.RPTETSHTEH.AQQS.PTD.TSEQ
Retrocopy TLQEGAPRSLGTGTL*NYNQACSEL*GETQSLSSL<SSLCGSP<HGRPTETSHTEHSAQQS<PTDMTSEQ

Parental  LRGDPGLRGNIL
          L.G...L.G...
Retrocopy L*GSGLLWGQLM

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	0.35 RPM	27.95 RPM
SRP017611_kidney	0.10 RPM	43.76 RPM
SRP017611_liver	0.17 RPM	39.22 RPM
SRP040447_lung	0.18 RPM	35.56 RPM
SRP040447_skeletal_muscle	0.01 RPM	10.40 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1391 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1391 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014046	1 retrocopy	retro_cpor_1391 ,
Myotis lucifugus	ENSMLUG00000011253	1 retrocopy	retro_mluc_1390,