RetrogeneDB ID: retro_cpor_204

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:28589533..28589872(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSCPOG00000000763
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 [Source:HGNC Symbol;Acc:864]

Sequence

>retro_cpor_204
TCTCAAGGAATTCAGCAGCTACTGCTAGCTGAGAAGTGGGCCGTGGAGAAGGTGTCTGAGGCCCGCAAGTGAAAGAACTG
AAGACTGAAGCAAGCCAAAGCAGCAGCTCACGCTGAGATTGAACAGTACTGCCCGCAGACAAAGAAAGGATTCAAGGCTA
AGGAAGCTGCGGCCTTAGGATCCCATGGAAGCTGAGCCGTGAAGTGGAGAAGGAGACCAGGAGAAGATGGCCGTCCTCCA
GAGCTACTTCCAGCAGAACAGGGAAGAGGTCCTGGATAACCTCTTGGCCTTTGTCTGCGCATCCGCCCAGAAATCCATGA
AAACTACCACTTCGATGGA

Alignment

ORF - retro_cpor_204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSHGS-CSSEV
          SQGIQQLL.AEK.A.EKVSEARK.KN.RLKQAK..A.AEIEQY..Q..K.FKAKEAAALGSHGS..S.EV
Retrocopy SQGIQQLLLAEKWAVEKVSEARK*KN*RLKQAKAAAHAEIEQYCPQTKKGFKAKEAAALGSHGS<LSREV

Parental  EKET-QEKMAVLQHYFQQNREEVLDNLLAFVC-DIRPEIHENYRING
          EKET.QEKMAVLQ.YFQQNREEVLDNLLAFVC..IRPEIHENY...G
Retrocopy EKET<QEKMAVLQSYFQQNREEVLDNLLAFVC<RIRPEIHENYHFDG

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	0.40 RPM	8.11 RPM
SRP017611_kidney	0.10 RPM	20.41 RPM
SRP017611_liver	0.26 RPM	21.15 RPM
SRP040447_lung	0.55 RPM	28.85 RPM
SRP040447_skeletal_muscle	0.10 RPM	20.58 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_204 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_204 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 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788, retro_cjac_2513, retro_cjac_76,
Cavia porcellus	ENSCPOG00000000763	5 retrocopies	retro_cpor_1523, retro_cpor_204 , retro_cpor_688, retro_cpor_742, retro_cpor_852,
Dasypus novemcinctus	ENSDNOG00000008083	15 retrocopies	retro_dnov_1173, retro_dnov_1447, retro_dnov_1475, retro_dnov_1504, retro_dnov_1588, retro_dnov_1645, retro_dnov_193, retro_dnov_1998, retro_dnov_2179, retro_dnov_218, retro_dnov_2416, retro_dnov_245, retro_dnov_336, retro_dnov_479, retro_dnov_790,
Dipodomys ordii	ENSDORG00000014850	5 retrocopies	retro_dord_434, retro_dord_466, retro_dord_614, retro_dord_640, retro_dord_749,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Myotis lucifugus	ENSMLUG00000008657	2 retrocopies	retro_mluc_373, retro_mluc_839,
Macaca mulatta	ENSMMUG00000004899	4 retrocopies	retro_mmul_1783, retro_mmul_2018, retro_mmul_2046, retro_mmul_331,
Monodelphis domestica	ENSMODG00000019574	1 retrocopy	retro_mdom_1675,
Mus musculus	ENSMUSG00000039105	5 retrocopies	retro_mmus_2028, retro_mmus_2784, retro_mmus_2787, retro_mmus_3316, retro_mmus_819,