RetrogeneDB ID: retro_ocun_949

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:55734037..55734456(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSOCUG00000012164
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) [Source:HGNC Symbol;Acc:843]

Sequence

>retro_ocun_949
ATGTTCGCCTGTGCCAGACTCGCCTGCACCCCTGCTCTGATCTGAGCTGGATCCAGAGTCGCATACAGACCAATTTCTGC
ATCAGTGTTGTCCCGACCAGAGGCCAGGACTGGAGAGGGCTCTACAGTATTTAATGGGGCCCAGAATGGTGTGTCTCAAC
TTATCCGAAGGGAGTTCAGACCAGTGCGATCAGCAAAGACATTGATACTGCTGCCAATTTTATTGGTGCAGGTGCTGCAA
CAGTAGGAGTGGCTGGTTCTGGTGCTGGTATTGGAACAGTTTTTGGCAGCCTCATCATTGGTTATGCCAGAAACCCTTCG
CTGAAGCAGCAGCTGTTCTCATATGCTATCCTGGGATTTGCCTTGTCTGAAGCTATGGGTCTCTTTTGTTTGATGGTTGC
TTTCTTGATTTTGTTTGCC

Alignment

ORF - retro_ocun_949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.45 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFACAKLACTPALIRAGSRVAYRPISASVLSRPEARTGEGSTVFNGAQNGVSQLIRREF-QTSAISRDID
          MFACA.LACTPALI.AGSRVAYRPISASVLSRPEARTGEGSTVFNGAQNGVSQLIRREF.QTSAIS.DID
Retrocopy MFACARLACTPALI*AGSRVAYRPISASVLSRPEARTGEGSTVFNGAQNGVSQLIRREF<QTSAISKDID

Parental  TAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILF
          TAA.FIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILF
Retrocopy TAANFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILF

Parental  A
          A
Retrocopy A

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	0.11 RPM	180.08 RPM
SRP017611_kidney	0.10 RPM	374.92 RPM
SRP017611_liver	0.23 RPM	82.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_949 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000008933	4 retrocopies	retro_ocun_1933, retro_ocun_450, retro_ocun_762, retro_ocun_794,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949 ,
Oryctolagus cuniculus	ENSOCUG00000016225	2 retrocopies	retro_ocun_346, retro_ocun_375,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,