RetrogeneDB ID: retro_cpor_714

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:2416349..2416743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP7
• Ensembl ID: ENSCPOG00000024405
• Aliases: None
• Description: None

Sequence

>retro_cpor_714
AACTTCCTGAAGGTGACAGAGCAAATTCTGGGTAATATATTTTCTAAAAATAACAAAGTAATGTATTCATATGGAAATTA
CTTGTTTCATTACATCTGCCAAGACAGGGTTGTATATCTTTGTACCGTTAAGGATGATTCTGAATGTTCCTGAGCCTTCA
ATTTTCTGATTAAGTAAGGAAGAGGTCCCATGCTACTTACAGTTCAAGAGCACATACAATACTTTCATTTGCCATGAATA
GCAAGTTCTCAACTGTCTTGCCTGCACAGATGAAACATCACTCTGAGACTAAGGACCTAGATGAAGTGATGGAGACTCAG
CCCAAAGGGATGAACTGAAAAGAATCATGGTCAGAAATATAGAACTCAACAATATAGCTCAACAAGGAGAAAGA

Alignment

ORF - retro_cpor_714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.91 %
• Parental protein coverage: 58.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NFLEVTEQILAKIPSENNKLTYSHGNYLFHYIC-DRIVYLCITDDDFERSRAFNFLNE-VKKRFQTTYGS
          NFL.VTEQIL..I.S.NNK..YS.GNYLFHYIC.DR.VYLC...DD.E.S.AFNFL...V.KR...TY.S
Retrocopy NFLKVTEQILGNIFSKNNKVMYSYGNYLFHYICQDRVVYLCTVKDDSECS*AFNFLIK<VRKRSHATYSS

Parental  RAQTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQ-AQVDELKGIMVRNIDL--VAQRGER
          RA.T.L..AMNS.FS.VL.AQ.KHHSE.K.LD.VMETQ.AQ.DELK.IMVRNI.L...AQ.GER
Retrocopy RAHTILSFAMNSKFSTVLPAQMKHHSETKDLDEVMETQ<AQRDELKRIMVRNIELNNIAQQGER

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	6.50 RPM
SRP017611_kidney	0.00 RPM	9.95 RPM
SRP017611_liver	0.00 RPM	6.49 RPM
SRP040447_lung	0.00 RPM	7.52 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.51 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_714 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_714 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016289	2 retrocopies	retro_cjac_1958, retro_cjac_2410,
Cavia porcellus	ENSCPOG00000024405	1 retrocopy	retro_cpor_714 ,
Mus musculus	ENSMUSG00000051412	1 retrocopy	retro_mmus_2131,
Oryctolagus cuniculus	ENSOCUG00000001270	1 retrocopy	retro_ocun_842,
Ictidomys tridecemlineatus	ENSSTOG00000025036	1 retrocopy	retro_itri_720,