RetrogeneDB ID: retro_cpor_1270

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_61:9686441..9687275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD8
• Ensembl ID: ENSCPOG00000015575
• Aliases: None
• Description: None

Sequence

>retro_cpor_1270
CCTGTATTTTGTTTATGGTACAGTTACAGGCCAAGAAAAGAACCTCTTATCACTTTTGTCTTTATTTTGGTGATGTGTCA
CAGCATCTATGCTTATGCCCACGGCTCAGCTCCTCACAATGAATACTCCATGCTGATTTCTTGTGGATTGATGAGATTGG
GAGCAGGAAATGTAGTGGTTGTTAGGTTCCTATATTGCTGATGTTACTTCCTTTCAGGAAAGGACAAGTTCTCTGACAAA
TACAAGTAAATTTCAAGCATTAGTTTTCACTCTAGGTCCAGTTTTTCAGACTTGTTTGCACTCATTGGAGAAAAGGGTGT
GACACGGCTTATGACTAAACTGAAGATAAACCTGTACACTGCCCCAGTTTTACTTGGCACCTTTCTGGGAGATTTAAAAT
TATTCTGATCTTCGCTGTATTAAGAAAACATCATGTGGATGACTCAGGACAACCGTGTAAAAATATTAATTATGAAGCAG
CAAACACAGATACGGTCCAGGTTTCACAAGGAAATATCACTCGAATCACTACTGTGGCCACCAGTGTCTTGTGCACTCTG
TTTCTCTCTGCCATTTTTGAAATTATTCTTACTCCATTGATAATGGATATGTGTGCTTGGACTCAAGAACAAACTGTGTC
ATAAAACAGGACCATACTTACTTCTCTTCGAGTTGAGGAAGTTGCTGTGTTCATGAGGGTTGAATTACTTTCCAAAATGA
TTGGTGTGCAGGTTCTTCTGCTGGGGGATTCCTTGTGGTATGGACTGTCTTCTTTACTGGGTACCTTGGGGAAATCAGTT
TTCTAAACTACAGTGGAAAGATTTACGTCATAAC

Alignment

ORF - retro_cpor_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 56.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PIFGLWSNYRPRREPLIISIFISVAANCLYAYVHVPASHNKYYMLIARGLVGFGAGNVAVVR-SYVAGAT
          P.F.LW..YRPR.EPLI...FI.V.....YAY.H..A.HN.Y.MLI..GL...GAGNV.VVR.SY.A..T
Retrocopy PVFCLWYSYRPRKEPLITFVFILVMCHSIYAYAHGSAPHNEYSMLISCGLMRLGAGNVVVVR>SYIADVT

Parental  SLQERTSSMANTSTCQALGFILGPVFQTC-FALIGDKGVTWDVIKLQINMYTAPVLLGAFLGVL-NIVLI
          S.QERTSS..NTS..QAL.F.LGPVFQTC.FALIG.KGVT....KL.IN.YTAPVLLG.FLG.L..I.LI
Retrocopy SFQERTSSLTNTSKFQALVFTLGPVFQTC<FALIGEKGVTRLMTKLKINLYTAPVLLGTFLGDL<KIILI

Parental  LAAFREHRVDDSGRPCNSINFEAANTDEVQISQGSIDQIAVVSTNVLFFVVLFIFALFETILTPLTMDMY
          .A..R.H.VDDSG.PC..IN.EAANTD.VQ.SQG.I..I..V.T.VL....LF..A.FE.ILTPL.MDM.
Retrocopy FAVLRKHHVDDSGQPCKNINYEAANTDTVQVSQGNITRITTVATSVL--CTLFLSAIFEIILTPLIMDMC

Parental  AWTQEQAVLYNGIILAGLGVEAVVVFLGVKLLSKMIGERAVLL-GGLLVIWAGFF-ILLPWGNQFPKIQW
          AWTQEQ.V..N..IL..L.VE.V.VF..V.LLSKMIG....LL.GG.LV.W..FF....PWGNQF.K.QW
Retrocopy AWTQEQTVS*NRTILTSLRVEEVAVFMRVELLSKMIGVQVLLL<GGFLVVWTVFF<YWVPWGNQFSKLQW

Parental  KDLHNN
          KDL..N
Retrocopy KDLRHN

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	9.84 RPM
SRP017611_kidney	0.00 RPM	7.12 RPM
SRP017611_liver	0.00 RPM	14.93 RPM
SRP040447_lung	0.00 RPM	7.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.57 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1270 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1270 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	ENSCPOG00000015575	1 retrocopy	retro_cpor_1270 ,
Myotis lucifugus	ENSMLUG00000005391	1 retrocopy	retro_mluc_1017,