RetrogeneDB ID: retro_cpor_1010

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:24207698..24208319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSCPOG00000013587
• Aliases: None
• Description: Isocitrate dehydrogenase [NADP] [Source:UniProtKB/TrEMBL;Acc:H0VP28]

Sequence

>retro_cpor_1010
TCTAAGAGTTAGCTTTTGTATCTGAGCACCAAAAACAGTATTCTGAAGAAATATGGATGTTTTTAAGGACATCTTTCAGG
AGATACATGACAAGCAGTGCAAATCCCAGTTTGAATCCCAGAAGACCCAGTATAAGCACACGCTCATCCATGATGGGTGG
TCCAAGGTATGAAGTCAGAAAGAGACTTCTGACTCCGTAAAAAAACTACAGTGATGACATACAATCAGATTCTGTTGCTC
AAGGCTATGGCTGCCTTGGCATGATAACCAGGTGTGCCGGTTTGTCCAGATGTCAAGATCATAGAAGCAGAGGCTGCCCA
TGGGACTGTAGCGTGCCACTACTTTATGTACCAGAGGATCAGGAGACCCCCTGCATTGCTTCCATTTTTGCCTGGACCAG
AGGGTCAGCCCACAGAACAAAGCTTGATAATGATACCAAACTCAGCTACTTTGCAAAATCTTTGGAAGAAGTCTGCATTG
AGACCATTTGCGGGTGGCTTCATGACCAGGGACTCGGCTGCTTGCATTAAAGGTTTACCCAGTGTACCACATTCTCACTA
CTTGAATACATTTGAGTTCATGGACAAACTTGGAGAAAACCTGAAGATAAAACTAGCTCAA

Alignment

ORF - retro_cpor_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.91 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SKGWPLYLSTKNTILKKYDGRF-KDIFQEIYDKQYKSQFEAQKIWYEHRLIDD-MVAQAMKSEGGF-IWA
          SK...LYLSTKN.ILKKY.G.F.KDIFQEI.DKQ.KSQFE.QK..Y.H.LI.D..V.Q.MKSE..F....
Retrocopy SKS*LLYLSTKNSILKKY-GCF>KDIFQEIHDKQCKSQFESQKTQYKHTLIHD<WVVQGMKSERDF<LTP

Parental  CKNYDGDVQSDSVAQGYGSLGMMT-SVLVCPDGKTVEAEAAHGTVTRHYRMYQK-GQETSTNPIASIFAW
          .KNY..D.QSDSVAQGYG.LGM.T..V.VCPD.K..EAEAAHGTV..HY.MYQ...QET....IASIFAW
Retrocopy *KNYSDDIQSDSVAQGYGCLGMIT>GVPVCPDVKIIEAEAAHGTVACHYFMYQR<DQETPC--IASIFAW

Parental  TRGLAHRAKLDNNKELDFFAKALEEVCIETI-EAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENL
          TRG.AHR.KLDN...L..FAK.LEEVCIETI...GFMT.D.AACIKGLP.V..S.YLNTFEFMDKLGENL
Retrocopy TRGSAHRTKLDNDTKLSYFAKSLEEVCIETI>AGGFMTRDSAACIKGLPSVPHSHYLNTFEFMDKLGENL

Parental  KTKLAQ
          K.KLAQ
Retrocopy KIKLAQ

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	0.12 RPM	16.51 RPM
SRP017611_kidney	0.00 RPM	313.96 RPM
SRP017611_liver	0.04 RPM	475.23 RPM
SRP040447_lung	0.00 RPM	37.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1010 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1010 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
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158, retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010 ,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328, retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549,