RetrogeneDB ID: retro_cpor_1286

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_65:2335420..2335943(+)
• Located in intron of: ENSCPOG00000009391

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11ORF54
• Ensembl ID: ENSCPOG00000014146
• Aliases: None
• Description: None

Sequence

>retro_cpor_1286
CCTGCAGATGAAGGAGACCTATTAGAGAAACACAACAATTCTGGATGTGCACTAATGACTAATCTTTTTGCCAGTGCGGG
TCAACCTGGGAAGGTAACTGAGGTAAAAGCCAAAATAAGAACTGGACAACTTAACTTTGTGACTTCTATGAGACAGACTC
TGGGAAACCATTATGGAAACAAGCCTGTAGGGATGGGAGATACTTTCACAGTTGAGAAGGGAAAACTAAAGGCTCATATT
ACGCACATAAAATTTTCTCCTTGTCTAATGAACTCTGATGAAGAAATAAATAAATGGCTGCATTTTTATGAAATGAAGGC
TTCTTTGGTTAGCCTACCAGTTTTTGTATCCAAAGACCCAGGGTTTGATTTGTGACTGACACACTCACTTTTTAGTCATC
ATGGAGAAGGTGGACACTACCATTAAGACACTTCTCCAGATACAGTGGAATACCTTGGGTACGTTTCACCTGCAGTTTCT
CTATCGCACTGATCAACCAAAAGAGACCCATGGCTTTGGGAGA

Alignment

ORF - retro_cpor_1286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.35 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PADGGYLLEKYNKKYHDFGCALMANLFASEGQPGKVIEVKAKRRTGQLNFVTSMRQTLGNHYGNKPVGMG
          PAD.G.LLEK.N......GCALM.NLFAS.GQPGKV.EVKAK.RTGQLNFVTSMRQTLGNHYGNKPVGMG
Retrocopy PADEGDLLEKHNNS----GCALMTNLFASAGQPGKVTEVKAKIRTGQLNFVTSMRQTLGNHYGNKPVGMG

Parental  GTFIVQKGKVKAHIMPTEFSSCPLNSDEEINKWLNFYEMKAPLVCLPVFVSKDPGFDLRLEHTHFFSHHG
          .TF.V.KGK.KAHI....FS.C..NSDEEINKWL.FYEMKA.LV.LPVFVSKDPGFDL.L.H...FSHHG
Retrocopy DTFTVEKGKLKAHITHIKFSPCLMNSDEEINKWLHFYEMKASLVSLPVFVSKDPGFDL*LTHS-LFSHHG

Parental  EGGHYHYDTTPDTVEYL-GYFSPAEFLYRIDQPKETHGFGR
          EGGHYH.DT.PDTVEYL.G.F....FLYR.DQPKETHGFGR
Retrocopy EGGHYH*DTSPDTVEYL>GTFH-LQFLYRTDQPKETHGFGR

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	13.46 RPM
SRP017611_kidney	0.10 RPM	203.83 RPM
SRP017611_liver	0.00 RPM	272.61 RPM
SRP040447_lung	0.00 RPM	10.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1286 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1286 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013446	1 retrocopy	retro_chof_593,
Cavia porcellus	ENSCPOG00000014146	1 retrocopy	retro_cpor_1286 ,
Monodelphis domestica	ENSMODG00000000412	2 retrocopies	retro_mdom_1467, retro_mdom_852,
Otolemur garnettii	ENSOGAG00000002523	1 retrocopy	retro_ogar_3359,
Tupaia belangeri	ENSTBEG00000007819	1 retrocopy	retro_tbel_4251,
Tursiops truncatus	ENSTTRG00000001140	3 retrocopies	retro_ttru_244, retro_ttru_334, retro_ttru_560,