RetrogeneDB ID: retro_ocun_639

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:26372591..26372941(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSOCUG00000026252
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 [Source:HGNC Symbol;Acc:864]

Sequence

>retro_ocun_639
ATGGCCAGCCAGTCGCAGGGGATCCAGCAGCTGCTGCAGGCCGAGAAGCAGGCGGCGGAGAATGTGTCGGAGGCCCGCAA
TTGAAAGAACCGGAGGCTGAAGCAGGCCAAAGAAGCACAGGCTGAAATTGAACAGTACCGCTTGCAGAGGGAGAAGGAGT
TCAAGGCCAAGGAAGCTGCGGTGCTGGGATCCCACGGCAGTTGCAGCAGCGAAGTAGAGAGGAGACCCAGGAGAAGATGA
CCATCCTGCAGACCTACTTCCAGCAGAACAGGGATGAGGTCTTGGATAACCTCTTGGCCTTTGTCTGTGACATCCGGCCA
GAAATCCATGAGAACTACCGCATAAACGGA

Alignment

ORF - retro_ocun_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSHGSCS
          MASQSQGIQQLLQAEK.AAE.VSEAR..KNRRLKQAKE.AQAEIEQYRLQREKEFKAKEAA.LGSHGSCS
Retrocopy MASQSQGIQQLLQAEKQAAENVSEARN*KNRRLKQAKE-AQAEIEQYRLQREKEFKAKEAAVLGSHGSCS

Parental  SEVEK-ETQEKMTILQTYFQQNRDEVLDNLLAFVCDIRPEIHENYRING
          SEVE..ETQEKMTILQTYFQQNRDEVLDNLLAFVCDIRPEIHENYRING
Retrocopy SEVER<ETQEKMTILQTYFQQNRDEVLDNLLAFVCDIRPEIHENYRING

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	0.28 RPM	52.87 RPM
SRP017611_kidney	0.71 RPM	64.16 RPM
SRP017611_liver	0.15 RPM	26.36 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_639 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012509	3 retrocopies	retro_amel_1053, retro_amel_376, retro_amel_999,
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788, retro_cjac_2513, retro_cjac_76,
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,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Felis catus	ENSFCAG00000000160	2 retrocopies	retro_fcat_1614, retro_fcat_402,
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,
Mustela putorius furo	ENSMPUG00000001653	3 retrocopies	retro_mputfur_1338, retro_mputfur_922, retro_mputfur_994,
Mus musculus	ENSMUSG00000039105	5 retrocopies	retro_mmus_2028, retro_mmus_2784, retro_mmus_2787, retro_mmus_3316, retro_mmus_819,
Oryctolagus cuniculus	ENSOCUG00000026252	3 retrocopies	retro_ocun_1411, retro_ocun_368, retro_ocun_639 ,