RetrogeneDB ID: retro_rnor_1246

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:304375..304669(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atp6v1g1
• Ensembl ID: ENSRNOG00000008163
• Aliases: None
• Description: V-type proton ATPase subunit G 1 [Source:RefSeq peptide;Acc:NP_001100130]

Sequence

>retro_rnor_1246
ATGGGCAATGACTCACAGGGCATCCAGCAGCTATTGCAGGCCGAGAAGCAGGCAGCTGAGAAGGTGTCCACGGCCTGAGA
GCCAAAAAACGAGAGGCTGAAGCAGGCCAAAGAAGCCCAGGCTGAAATTGAACAGTACGTCCTGCAGAGGGAGAAGGAGT
TCAAGGCTAAGGAAGCTGCAGCACTGGGGACCCATGGCAGTTGTAGCAGAGAGGTGGAAAAGTAGACCCAGGAGCAGAGG
ACTATCCTCCAGAACTACTTCGAGCAGAACAGGGATTAAGTCCTGGATAACCTT

Alignment

ORF - retro_rnor_1246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.83 %
• Parental protein coverage: 83.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSHGSCS
          M...SQGIQQLLQAEK.AAEKVS.A...KN.RLKQAKE.AQAEIEQY.LQREKEFKAKEAAALG.HGSCS
Retrocopy MGNDSQGIQQLLQAEKQAAEKVSTA*EPKNERLKQAKE-AQAEIEQYVLQREKEFKAKEAAALGTHGSCS

Parental  SEVEKETQEKMTILQNYFEQNRDEVLDNL
          .EVEK.TQE..TILQNYFEQNRD.VLDNL
Retrocopy REVEK*TQEQRTILQNYFEQNRD*VLDNL

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	0.36 RPM	82.11 RPM
SRP017611_kidney	0.98 RPM	106.00 RPM
SRP017611_liver	0.34 RPM	51.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1246 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1246 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Equus caballus	ENSECAG00000011155	1 retrocopy	retro_ecab_816,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Microcebus murinus	ENSMICG00000015368	3 retrocopies	retro_mmur_1217, retro_mmur_1259, retro_mmur_755,
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,
Otolemur garnettii	ENSOGAG00000010103	3 retrocopies	retro_ogar_1824, retro_ogar_2822, retro_ogar_342,
Pteropus vampyrus	ENSPVAG00000008334	1 retrocopy	retro_pvam_1432,
Rattus norvegicus	ENSRNOG00000008163	2 retrocopies	retro_rnor_1246 , retro_rnor_676,
Tursiops truncatus	ENSTTRG00000015203	2 retrocopies	retro_ttru_125, retro_ttru_480,