RetrogeneDB ID: retro_ocun_1253

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:34966481..34966929(-)
• Located in intron of: ENSOCUG00000026872

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC1
• Ensembl ID: ENSOCUG00000009369
• Aliases: None
• Description: voltage-dependent anion channel 1 (VDAC1), nuclear gene encoding mitochondrial protein, mRNA [Source:RefSeq mRNA;Acc:NM_001082075]

Sequence

>retro_ocun_1253
GTAGATTTCAACATTGTTGGGCCCTTCATTCAGGATGCTTTGGTGCTGTGTTACCAAGGCCGGTTTGGCTGGCTACCAGA
TGAACTCTGGGAGTGCAAAGTCCCAGGTCACGCAGAGCAACTTTACCATCAGCTACAAGAGTGACAGATTCCAGCTTAAC
AATGGAACAGAGTTTGGCTGCTCCATTTACCAAAAGGTAAACAAGAAGGTGGAGACTGTGGTCAGTCTTGCCTGGACAGC
AGGAAACTAATGTTCCAGAATAGCAGCCAATTATCAGATCTGCCATGACACTTGCTTCTCGGCTAAGGTGAACAACTCCA
GCTTGATAGGATTAAGATACACTCAGACTCCAACGCCAGGTATCAGACTGATGCAGTCAGCTCTGCTGGGTGGCAAGAAC
ATCAATACTGGTGGCCACAGGCTTGTTCTAGGACTGGAATCTCAAGCA

Alignment

ORF - retro_ocun_1253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 54.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDFDIAGPSIRGALVLGYEG-WLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQK
          VDF.I.GP.I..ALVL.Y.G..LAGYQMN...AKS.VTQSNF...YK.D.FQL....N.GTEFG.SIYQK
Retrocopy VDFNIVGPFIQDALVLCYQG>GLAGYQMNSGSAKSQVTQSNFTISYKSDRFQL----NNGTEFGCSIYQK

Parental  VNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKN
          VNKK.ET.V.LAWTAGN...R..IAA.YQI..D.CFSAKVNNSSLIGL.YTQT..PGI.L..SALL.GKN
Retrocopy VNKKVETVVSLAWTAGN*CSR--IAANYQICHDTCFSAKVNNSSLIGLRYTQTPTPGIRLMQSALLGGKN

Parental  VNAGGHKLGLGLEFQA
          .N.GGH.L.LGLE.QA
Retrocopy INTGGHRLVLGLESQA

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	0.17 RPM	195.42 RPM
SRP017611_kidney	0.51 RPM	215.99 RPM
SRP017611_liver	0.23 RPM	71.83 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1253 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013556	8 retrocopies	retro_cjac_1216, retro_cjac_1669, retro_cjac_1728, retro_cjac_2677, retro_cjac_3183, retro_cjac_3864, retro_cjac_454, retro_cjac_907,
Cavia porcellus	ENSCPOG00000023840	2 retrocopies	retro_cpor_1061, retro_cpor_699,
Dipodomys ordii	ENSDORG00000000714	1 retrocopy	retro_dord_636,
Felis catus	ENSFCAG00000008421	1 retrocopy	retro_fcat_1592,
Gorilla gorilla	ENSGGOG00000010880	3 retrocopies	retro_ggor_693, retro_ggor_875, retro_ggor_981,
Macaca mulatta	ENSMMUG00000016235	6 retrocopies	retro_mmul_1023, retro_mmul_1070, retro_mmul_1305, retro_mmul_1851, retro_mmul_2417, retro_mmul_2613,
Monodelphis domestica	ENSMODG00000014157	1 retrocopy	retro_mdom_1120,
Mustela putorius furo	ENSMPUG00000010220	1 retrocopy	retro_mputfur_83,
Mus musculus	ENSMUSG00000020402	3 retrocopies	retro_mmus_2013, retro_mmus_3079, retro_mmus_3124,
Oryctolagus cuniculus	ENSOCUG00000009369	3 retrocopies	retro_ocun_1253 , retro_ocun_1428, retro_ocun_583,
Otolemur garnettii	ENSOGAG00000030742	2 retrocopies	retro_ogar_1197, retro_ogar_2876,
Rattus norvegicus	ENSRNOG00000006375	8 retrocopies	retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947,
Sorex araneus	ENSSARG00000008221	6 retrocopies	retro_sara_115, retro_sara_327, retro_sara_355, retro_sara_533, retro_sara_668, retro_sara_702,
Ictidomys tridecemlineatus	ENSSTOG00000007764	3 retrocopies	retro_itri_1137, retro_itri_1506, retro_itri_693,
Tupaia belangeri	ENSTBEG00000003852	4 retrocopies	retro_tbel_1282, retro_tbel_2613, retro_tbel_3818, retro_tbel_4546,
Tarsius syrichta	ENSTSYG00000007346	1 retrocopy	retro_tsyr_161,