RetrogeneDB ID: retro_cpor_1054

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_41:8920580..8920994(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSCPOG00000003705
• Aliases: None
• Description: None

Sequence

>retro_cpor_1054
CAGATGGATTGGCTACAGGGAGTCAACCAGTTTGGGAACAAGTATATTCAGCAGACCAAGCCCCTCACCTTGGAGCACAC
CATCTACCTGTACTCTCTTACTAACTACCCTTTTGGTATGAAAGTGCCCCTCAATGAAAAGGACAGCTCAGTTGCAGCCA
ACTTTCTATGCATGAGAGAAGAATTTGATAAAATTGGATTGAGGAAGATTATAAAACAGGTTCTGATTGTACTTGAGCAC
CAGCTTCCCCATATGTGACTATTACAGCTGGGAACAACTTTCTTCAAATTACCTGGTTGTGAACTTAATCCAGGAAAAGA
TGAAGTTGAAGGACTAAAACACTTAATGACAGAGATACTGAGTCGCCAGGATGGAGTCCTGCCAGACTGGGTCATTGATT
ACTGCACTGGTAAC

Alignment

ORF - retro_cpor_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 60.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRT
          Q..W..GVNQFGNKYIQQTKPLTLE.TI.LY.LTNY.FG.K.PL.EKDSSVAA.F..MREEFDKIG.R..
Retrocopy QMDWLQGVNQFGNKYIQQTKPLTLEHTIYLYSLTNYPFGMKVPLNEKDSSVAANFLCMREEFDKIGLRKI

Parental  VEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGN
          ...VLIV.EH.LPH..LLQLGTTFFKLPG.ELNPG.DEVEGLK.LMTEIL.RQDGVL.DWVID.C.GN
Retrocopy IKQVLIVLEHQLPHM*LLQLGTTFFKLPGCELNPGKDEVEGLKHLMTEILSRQDGVLPDWVIDYCTGN

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	19.56 RPM
SRP017611_kidney	0.00 RPM	21.88 RPM
SRP017611_liver	0.00 RPM	15.41 RPM
SRP040447_lung	0.00 RPM	18.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.35 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1054 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1054 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054 ,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,