RetrogeneDB ID: retro_cpor_1114

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_47:2938689..2939056(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000011774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUB1
• Ensembl ID: ENSCPOG00000005584
• Aliases: None
• Description: None

Sequence

>retro_cpor_1114
ATGCCTAAATCAAAGGAACTTGTTCCTTCAAGCTCTTCAGGCAATGATTCCGACAGTGAAGTTGACAAAAAGTTAAAGAG
GAAAAAGCTCCAGAAAAACCTGTAAAGAAGCAAAACACTGGTGAGACTCTGAGGACTCTGTCGCCATCTAAGCCGAGCAG
CAGCAGGAGGATAACATGTTCCAGATTGGAAAAATGAGGTATGTCAGTGTTCGGGGCTTTACAGGCAAAGTTCTAATTGA
TATTAGAGAATCTTGGATGGATCCAGAAGGTGGAATGAAACCAGGAAGAAAAGGTGTTTCTTTAAATCCAGAGCAGTGGA
GCCAGCTGAAGGAGCACATTTCTGACATTGATGAGGCAGTAAGAAAA

Alignment

ORF - retro_cpor_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKSKELVSSSSSGSDSDSEVD-KKLKRKKQVAPEKPVKKQKTGETSRALSSSKQSSSSR-DDNMFQIGK
          MPKSKELV.SSSSG.DSDSEVD..K.K..K..APEKPVKKQ.TGET.R.LS.SK.SS.SR..DNMFQIGK
Retrocopy MPKSKELVPSSSSGNDSDSEVD<QKVKEEK--APEKPVKKQNTGETLRTLSPSKPSS-SR<EDNMFQIGK

Parental  MRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRK
          MRYVSVR.F.GKVLIDIRE.WMDPEG.MKPGRKG.SLNPEQWSQLKE.ISDID.AVRK
Retrocopy MRYVSVRGFTGKVLIDIRESWMDPEGGMKPGRKGVSLNPEQWSQLKEHISDIDEAVRK

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	68.39 RPM
SRP017611_kidney	0.00 RPM	38.84 RPM
SRP017611_liver	0.00 RPM	50.53 RPM
SRP040447_lung	0.00 RPM	34.86 RPM
SRP040447_skeletal_muscle	0.00 RPM	15.16 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1114 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1114 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 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018879	5 retrocopies	retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus	ENSCJAG00000018718	2 retrocopies	retro_cjac_1908, retro_cjac_484,
Cavia porcellus	ENSCPOG00000005584	4 retrocopies	retro_cpor_1114 , retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus	ENSDNOG00000007611	5 retrocopies	retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Homo sapiens	ENSG00000113387	2 retrocopies	retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla	ENSGGOG00000027033	3 retrocopies	retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana	ENSLAFG00000011006	1 retrocopy	retro_lafr_19,
Macropus eugenii	ENSMEUG00000007770	4 retrocopies	retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus	ENSMICG00000014535	2 retrocopies	retro_mmur_1115, retro_mmur_17,
Myotis lucifugus	ENSMLUG00000013685	6 retrocopies	retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta	ENSMMUG00000011470	2 retrocopies	retro_mmul_2318, retro_mmul_993,
Monodelphis domestica	ENSMODG00000020410	3 retrocopies	retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furo	ENSMPUG00000015185	2 retrocopies	retro_mputfur_186, retro_mputfur_295,
Mus musculus	ENSMUSG00000022205	4 retrocopies	retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus	ENSOCUG00000006262	5 retrocopies	retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii	ENSOGAG00000009012	6 retrocopies	retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Pongo abelii	ENSPPYG00000015379	2 retrocopies	retro_pabe_124, retro_pabe_1371,
Rattus norvegicus	ENSRNOG00000050563	12 retrocopies	retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii	ENSSHAG00000014986	1 retrocopy	retro_shar_628,
Tarsius syrichta	ENSTSYG00000014069	2 retrocopies	retro_tsyr_528, retro_tsyr_895,