RetrogeneDB ID: retro_ecab_816

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:63150482..63150815(-)
• Located in intron of: ENSECAG00000022057

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSECAG00000011155
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 [Source:HGNC Symbol;Acc:864]

Sequence

>retro_ecab_816
AGTCAGTTGAAAGGCATCTAGCAGCTGCAGGATGAGAAGTGGGCCACACAGAAGATGTCTGAGGCCTACAAGCAAAAGAA
CCTGAAGCTGAAGCAGGACAAAGAAGCTTAGGCTGAAGTTTAACCGTACCACCTGCAGGAGAAAGGGTTCAGGGCCAAGG
AAGCTGTGCCTCTGGGATCCCATGACAGCTGCAACACCGAAGTGGAGAAGGAGACCCAGGAGATGACCATCCTCCAGACC
TACTTCCGGCAGCACACGTATGAAGTTCCGGATAACCTCTTGGCCTTTGTTTGCAACATCTGGCTAGAAATCCATGAAAA
CTACCACATAAAT

Alignment

ORF - retro_ecab_816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.28 %
• Parental protein coverage: 98.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQSQGQQLLQSEKRAA-KVSEDRKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSHGSCSSEV
          SQ..G...LQ.EK.A..K.SE..K.KN..LKQ.KE.A.AE...Y.LQ.EK.F.AKEA..LGSH.SC..EV
Retrocopy SQLKGI*QLQDEKWATQKMSEAYKQKNLKLKQDKE-A*AEV*PYHLQ-EKGFRAKEAVPLGSHDSCNTEV

Parental  EKETQQKMSILQTYFRQNRDEVLDDLLAFVCDIRPEIHENYRLN
          EKETQ..M.ILQTYFRQ...EV.D.LLAFVC.I..EIHENY..N
Retrocopy EKETQE-MTILQTYFRQHTYEVPDNLLAFVCNIWLEIHENYHIN

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
SRP021940_articular_cartilage	0.00 RPM	15.82 RPM
SRP021940_cerebellum	0.00 RPM	62.37 RPM
SRP021940_embryo	0.00 RPM	48.26 RPM
SRP021940_placental_villous	0.00 RPM	102.09 RPM
SRP021940_synovial_membrane	0.00 RPM	39.28 RPM
SRP021940_testis	0.00 RPM	108.38 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_816 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_816 has 0 orthologous retrocopies within eutheria group .

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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,