RetrogeneDB ID: retro_cpor_293

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:48473100..48474130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013878
• Aliases: None
• Description: None

Sequence

>retro_cpor_293
AGCTGCATGAAGAGGAAAAAGTTTCACATGTAGCGCTCAGATGCCTCCACTCTGATGCGCAACCCATTCAGCCTCATCCT
GGTGAATACCAACAGTGACCGACTATTCACAGTGAACGAGGTTGATGTTGGTGGCTCAAAGTGTGGCATCATCAGGCCGA
GGGGTATGAAGATGCCTGCATTCAAGATGCACACACATAACTTCTACTTCACCAACCGCAAGATGAATTCTGTGTGCTGG
GCTTTGCTGAACCACTTGGATTCCCATGTTCTGCTGTGCCTCTTGGGATTTGCAGAGACTAGAGGCTGTGCCACTCTGAT
CCAGCATCACTGTTTACCGGTAGTCACCCAGGTGTAGACTTCTGTGGCATGCTTGCAGTTTCTGGATCCCTGGTGCCTGG
TCCTATGCATGCATGGTGGCTGAACATTCAGGTAAACACTTGCTTCAGTACCTGTTGTCTCAGGTGATTCTGTTGATCAG
TGCAGTGACAGGACACTGGCAGTCATTCAGGACCAACCGTGCTATGTTGGCCCAGCAGTTTGCTGTCATGACTCCTTTGC
TCTTTAGTGACTGTCTCTCTGGGGACATCTTTGCCATTGATCTGCATTCTTGAACTCAAGGTAAAGCCTGGAAGGCTGCC
TGCCTACTCCATCACTCAGCAGTGACCTCTTTGTGGATCCTCCAGGAAGAGCAATCTGTGTTGGTATCAGATATGCTGGG
AAAGATCAAGCTGTAGGACCTATGGACCATGAAGTGTATAAGGCAGTACAAAGGTCATGAGAATGAGTATGCCTGCCTGC
CCTTGCATGTGCACGAGGAAGAAAGAATCCTGAAGGCAGTATGCCAGGACAGCTACACAAGAATCTGGAGCCTCCATGAT
GCCCACCTGCTCAGAACCACACCCTACTTGCATCCTATCTCCAATACTAACATTCCCAGTATGGCCTTCTCTTTTCGGCT
TAGAGGAGTTGAAGGATCCCCACGGCTGCTCATGGCCCTCAAGCAGGACCTTTACTGTTTCTCCGACAGC

Alignment

ORF - retro_cpor_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.68 %
• Parental protein coverage: 69.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SCMEKKKVHIQSAESSTVISDPFSLILADTNSDRLFTVNDVDVGGSKYGVINLSGLKTPALEVHMHKNFY
          SCM..KK.H......ST....PFSLIL..TNSDRLFTVN.VDVGGSK.G.I...G.K.PA...H.H.NFY
Retrocopy SCMKRKKFHM*RSDASTLMRNPFSLILVNTNSDRLFTVNEVDVGGSKCGIIRPRGMKMPAFKMHTH-NFY

Parental  FTNRKVNSVCWASLNHLDSHVLLCLLGFAETPGCATLI-PASLFTSSHPGVDRRGMLC--SFRIPGAWSC
          FTNRK.NSVCWA.LNHLDSHVLLCLLGFAET.GCATLI.PASLFT.SHPGVD..GML.......PG....
Retrocopy FTNRKMNSVCWALLNHLDSHVLLCLLGFAETRGCATLI<PASLFTGSHPGVDFCGMLAVSGSLVPGPMH-

Parental  AWCLNVQANTCFSTG-LSRRILLTDVVTGHRQSYKTNSDVLAQQFAILTPLLFNGCRSGEIFAIDLRSRS
          AW.LN.Q.NTCFST..LS..ILL...VTGH.QS..TN...LAQQFA..TPLLF..C.SG.IFAIDL.S..
Retrocopy AWWLNIQVNTCFSTC<LSQVILLISAVTGHWQSFRTNRAMLAQQFAVMTPLLFSDCLSGDIFAIDLHS*T

Parental  QGKSWKTTCLFHDSAVTSLRILQEEQSILASDMAGKIKLWDLRNKKCIRQYEGHVNEYACLPLHVHEEEG
          QGK.WK..CL.H.SAVTSL.ILQEEQS.L.SDM.GKIKL.DL...KCIRQY.GH.NEYACLPLHVHEEE.
Retrocopy QGKAWKAACLLHHSAVTSLWILQEEQSVLVSDMLGKIKL*DLWTMKCIRQYKGHENEYACLPLHVHEEER

Parental  ILVAVGQDCYTRIWSLHDAHLLRTIPSPYPTSKADIPSVAFSSQFGGVQGSPGLLMAVRQDLYYFSYS
          IL.AV.QD.YTRIWSLHDAHLLRT.P...P.S...IPS.AFS....GV.GSP.LLMA..QDLY.FS.S
Retrocopy ILKAVCQDSYTRIWSLHDAHLLRTTPYLHPISNTNIPSMAFSFRLRGVEGSPRLLMALKQDLYCFSDS

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	46.88 RPM
SRP017611_kidney	0.00 RPM	51.92 RPM
SRP017611_liver	0.00 RPM	23.37 RPM
SRP040447_lung	0.00 RPM	60.23 RPM
SRP040447_skeletal_muscle	0.00 RPM	31.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_293 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_293 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013878	1 retrocopy	retro_cpor_293 ,
Homo sapiens	ENSG00000119599	2 retrocopies	retro_hsap_101, retro_hsap_92,
Gorilla gorilla	ENSGGOG00000003815	2 retrocopies	retro_ggor_2026, retro_ggor_2743,
Macaca mulatta	ENSMMUG00000003625	2 retrocopies	retro_mmul_152, retro_mmul_264,
Nomascus leucogenys	ENSNLEG00000002449	2 retrocopies	retro_nleu_1912, retro_nleu_833,
Pan troglodytes	ENSPTRG00000006507	2 retrocopies	retro_ptro_2774, retro_ptro_46,