RetrogeneDB ID: retro_cpor_1195

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_54:8810942..8811193(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYCBP
• Ensembl ID: ENSCPOG00000020447
• Aliases: None
• Description: None

Sequence

>retro_cpor_1195
GCTACGGTCTCTGGCACCAGCTACCCCACTGTCCCTGTCACTATGGCCCATTGCAAAGCTGCCGAATTGAATATTGAACA
GTTCTGGAAGTACATGGAGAAGTCGGGGGTGCTGGACACATTTACCAAGGTGTTGGTAGCCTTATATGAAGAACCATAGG
AACCTAATAGTGCTTTGGATTTTTAAAAGCATCATTTAGGAGCTGTACCCCAGAAAATCCAGAAATCAAGCTGCTTTGCC
TAGAATTGGCA

Alignment

ORF - retro_cpor_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATVSGASYAVAPVTMAHYKAADSKREQFRRYLEKSGVLDTLTKVLVALYEEPEKPNSALDFLKHHLGA-A
          ATVSG.SY...PVTMAH.KAA....EQF..Y.EKSGVLDT.TKVLVALYEEP..PNSALDF.KHHLGA..
Retrocopy ATVSGTSYPTVPVTMAHCKAAELNIEQFWKYMEKSGVLDTFTKVLVALYEEP*EPNSALDF*KHHLGA<C

Parental  TPENPEIELLRLELA
          TPENPEI.LL.LELA
Retrocopy TPENPEIKLLCLELA

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	1.61 RPM
SRP017611_kidney	0.00 RPM	10.47 RPM
SRP017611_liver	0.00 RPM	14.36 RPM
SRP040447_lung	0.03 RPM	5.27 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1195 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1195 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 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030622	1 retrocopy	retro_cfam_1618,
Choloepus hoffmanni	ENSCHOG00000013136	3 retrocopies	retro_chof_1349, retro_chof_151, retro_chof_610,
Callithrix jacchus	ENSCJAG00000036558	1 retrocopy	retro_cjac_5,
Cavia porcellus	ENSCPOG00000020447	1 retrocopy	retro_cpor_1195 ,
Homo sapiens	ENSG00000214114	2 retrocopies	retro_hsap_1649, retro_hsap_2251,
Gorilla gorilla	ENSGGOG00000005810	2 retrocopies	retro_ggor_1245, retro_ggor_1678,
Loxodonta africana	ENSLAFG00000020514	2 retrocopies	retro_lafr_1071, retro_lafr_903,
Macropus eugenii	ENSMEUG00000000315	1 retrocopy	retro_meug_247,
Mus musculus	ENSMUSG00000028647	1 retrocopy	retro_mmus_1626,
Nomascus leucogenys	ENSNLEG00000011814	2 retrocopies	retro_nleu_1319, retro_nleu_2489,
Oryctolagus cuniculus	ENSOCUG00000022203	2 retrocopies	retro_ocun_907, retro_ocun_979,
Otolemur garnettii	ENSOGAG00000024435	3 retrocopies	retro_ogar_1283, retro_ogar_1553, retro_ogar_1880,
Pongo abelii	ENSPPYG00000001515	1 retrocopy	retro_pabe_1400,
Pan troglodytes	ENSPTRG00000000565	2 retrocopies	retro_ptro_1120, retro_ptro_1594,
Rattus norvegicus	ENSRNOG00000017166	2 retrocopies	retro_rnor_573, retro_rnor_779,
Sus scrofa	ENSSSCG00000003649	2 retrocopies	retro_sscr_1176, retro_sscr_1217,
Ictidomys tridecemlineatus	ENSSTOG00000021547	2 retrocopies	retro_itri_1518, retro_itri_252,
Tarsius syrichta	ENSTSYG00000005690	1 retrocopy	retro_tsyr_172,
Tursiops truncatus	ENSTTRG00000009583	1 retrocopy	retro_ttru_1872,