RetrogeneDB ID: retro_cpor_1474

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:38398655..38399161(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO17
• Ensembl ID: ENSCPOG00000000656
• Aliases: None
• Description: F-box protein 17 [Source:HGNC Symbol;Acc:18754]

Sequence

>retro_cpor_1474
CGGCCTCCAAGGGTGGGGCCGCCCGGGTTCCCACACCGCAGTCGCAGCCCTCAAAGGGGCTAGATCTGAGCCGGCTGCCG
CCGGAGCTCCTCCCGACTGTGCTGAGCCACGTGCCCCCGCGCGTGCGGCTCCGACGCTGCTGTCTCGTGTGCCGTAGCTG
GCGGGCCCTGGTGGATGGCCAGGCCCTGTGGCTGCTGATCTTGGCCCAGGACCACAGCGCCACCGGCCGCGCCCTGCTGT
CCCTCGTCCGCAGTTGCCTGCCCCCTGCCGGCGACACCAACCCCTGCCCTCTCGGCCGCTTCTGCGAGCGCAGACCCATT
GGAGGAAACCTCATCTGCAACCCCTGCGGACAGGAAGGCCTTCGGAAGTGGATGGTGTAGCATGGTGGAGATGGCTGGGT
GGTGGAGGAAAATATGACAACCGTGCCTGGGGCCTCTTCGCAGACCTGCTTTGTAGCCTCCTTCAGTTGGTGTCGGAAGA
AGCAGGTCTTGGATCTGGAGGAGGAG

Alignment

ORF - retro_cpor_1474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.45 %
• Parental protein coverage: 57.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTPAVAMGGRPSR-QRQPVHPPATLDALPPELLVRVLSHVPPRALVTCCRPVCRAWRDVVDGPTVWLLQL
          R.P.V...G.P.R.Q.QP......L..LPPELL..VLSHVPPR.....C..VCR.WR..VDG...WLL.L
Retrocopy RPPRVGPPGFPHR<QSQP-SKGLDLSRLPPELLPTVLSHVPPRVRLRRCCLVCRSWRALVDGQALWLLIL

Parental  ARDRSAEGRAIYALAQRCPPSSENEEELPLCALARFCVRAPLGRNLIFNSCGEQGFRGWEVEHGGNGWAV
          A.D.SA.GRA...L...C.P..........C.L.RFC.R.P.G.NLI.N.CG..G.R.W.V.HGG.GW.V
Retrocopy AQDHSATGRALLSLVRSCLPPAGDTNP---CPLGRFCERRPIGGNLICNPCGQEGLRKWMV*HGGDGWVV

Parental  EKNITLVPGAPSQTCFVTSFEWCFKRQLVDLVME
          E.N.T.VPGA.SQTCFV.SF.WC.K.Q..DL..E
Retrocopy EENMTTVPGASSQTCFVASFSWCRKKQVLDLEEE

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	0.86 RPM	2.47 RPM
SRP017611_kidney	0.84 RPM	4.50 RPM
SRP017611_liver	0.13 RPM	0.22 RPM
SRP040447_lung	3.28 RPM	9.56 RPM
SRP040447_skeletal_muscle	0.43 RPM	3.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1474 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1474 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008717	1 retrocopy	retro_amel_1109,
Cavia porcellus	ENSCPOG00000000656	1 retrocopy	retro_cpor_1474 ,
Cavia porcellus	ENSCPOG00000004611	1 retrocopy	retro_cpor_1475,