RetrogeneDB ID: retro_cpor_312

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:45735865..45736228(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND1
• Ensembl ID: ENSCPOG00000014075
• Aliases: None
• Description: None

Sequence

>retro_cpor_312
TTGATGAAATTAAAGATGCATACTGATGGGGATAAATCACCTCCACAGGCAGAAAGAATTTGCTTCCAGTCTTTCTTACC
TAAGGACAAAGATAAGAGCAAATCTATTTTCTTTGCCATCAGTGGAGCACTGGCAATGCTACAGACTTTGCACCTTCACT
TGCCAATCTTAAAAAAGACAGTAACAAATTAACAGCTAAGAAGTTAAATGTTGTGTCATATTTCTTCAGGAGAAGGCTTA
CCCTTGAATTATGCTTTGGAAAGCTGGATAGCTAAGGAGTGTCCTTTATATAATGGTGGACACACTACTTTGAATTATCT
AAATAATGATGAATAGTCTTTAAAAAGTGTTGATTCTTCCTTG

Alignment

ORF - retro_cpor_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.6 %
• Parental protein coverage: 82. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMKLKMHADGDKSLPQAERIYFQVFLPKGSKDKSKPMFF-CHRWSIGKVIDFAASLASLKNDNNKLAAKK
          LMKLKMH.DGDKS.PQAERI.FQ.FLPK..KDKSK..FF.CH.WS.G...DFA.SLA.LK.D.NKL.AKK
Retrocopy LMKLKMHTDGDKSPPQAERICFQSFLPK-DKDKSKSIFF<CHQWSTGNATDFAPSLANLKKDSNKLTAKK

Parental  LR-LCHISSGEALPLDHSLETWLAKEDCPLYNGGNIILEYLNDDEQYLKNIDSYL
          L..LCHISSGE.LPL...LE.W.AKE.CPLYNGG...L.YLN.DE..LK..DS.L
Retrocopy LN>LCHISSGEGLPLNYALESWIAKE-CPLYNGGHTTLNYLNNDE*SLKSVDSSL

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	2.82 RPM
SRP017611_kidney	0.00 RPM	3.98 RPM
SRP017611_liver	0.00 RPM	4.18 RPM
SRP040447_lung	0.00 RPM	2.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_312 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_312 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014075	1 retrocopy	retro_cpor_312 ,
Homo sapiens	ENSG00000104231	1 retrocopy	retro_hsap_187,
Gorilla gorilla	ENSGGOG00000023665	1 retrocopy	retro_ggor_268,
Microcebus murinus	ENSMICG00000016889	1 retrocopy	retro_mmur_1073,
Macaca mulatta	ENSMMUG00000002626	1 retrocopy	retro_mmul_394,
Mus musculus	ENSMUSG00000039795	1 retrocopy	retro_mmus_2093,
Nomascus leucogenys	ENSNLEG00000002584	1 retrocopy	retro_nleu_997,
Otolemur garnettii	ENSOGAG00000009813	2 retrocopies	retro_ogar_2608, retro_ogar_514,
Tupaia belangeri	ENSTBEG00000015393	1 retrocopy	retro_tbel_3648,