RetrogeneDB ID: retro_cpor_1224

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_59:442302..442745(-)
• Located in intron of: ENSCPOG00000020088

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSCPOG00000010577
• Aliases: None
• Description: None

Sequence

>retro_cpor_1224
CTCAGCTGGGAAAATTTACAGTGGCTTCCAGAACTTGCCATCAATTCCCTGGGAGACCAGATAATCAGTGTCTTCTTTCT
AGATGGTAAGGATCAGGTGAATTCCTATGGATTCACAACAATTTTGGCTCATTTCTGACCCATTGACAGTGATACAAAGA
ACAAAGATGTGAATGGGTCAGAACCACTCAACAGCTGGATCAGCACCTACACTTTGCTTTTCAACTATACCGTGTGGATA
AAGATGGTAAGATTCCACATAGTGAGCTGTTAGCAGTGCTACGCATGATGGTCAGGGTGACTGTCTCAGGTGAGCAACTG
GGCATTGTCACAGACAGGGTCATCTGGGAAGTGGACCAACATGGAGACGGCACCGTATCTGTTAAATAATTTGTTAAGGT
TATGGAGAAAGTGAATATAGAACAGAAAATGAGCACCCGGTTT

Alignment

ORF - retro_cpor_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.07 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSREDFQRIPELAINPLGDRIINAFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNS-RSNK
          LS.E..Q..PELAIN.LGD.II..FF..G.DQVN..GF...LAHF.PI....K.KDVNG.EPLNS.....
Retrocopy LSWENLQWLPELAINSLGDQIISVFFLDGKDQVNSYGFTTILAHF*PIDSDTKNKDVNGSEPLNS<LDQH

Parental  LHFAFRLYDLDKDDKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVD
          LHFAF.LY..DKD.KI...ELL.VLRMMV.V..S.EQLG...DR.I.E.DQ.GD...S...FVKV.EKV.
Retrocopy LHFAFQLYRVDKDGKIPHSELLAVLRMMVRVTVSGEQLGIVTDRVIWEVDQHGDGTVSVK*FVKVMEKVN

Parental  VEQKMSIRF
          .EQKMS.RF
Retrocopy IEQKMSTRF

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	47.57 RPM
SRP017611_kidney	0.00 RPM	54.12 RPM
SRP017611_liver	0.00 RPM	66.16 RPM
SRP040447_lung	0.00 RPM	23.91 RPM
SRP040447_skeletal_muscle	0.00 RPM	14.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1224 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1224 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224 , retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,