RetrogeneDB ID: retro_ocun_352

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:28082957..28083976(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000008575
• Aliases: SLC2A3, GLUT3, SLC2A14
• Description: Solute carrier family 2, facilitated glucose transporter member 3 [Source:UniProtKB/TrEMBL;Acc:G1TI27]

Sequence

>retro_ocun_352
GTGGCCATCTTCTCTGTTAAGGCATGATTGGCTTATTTTCTGTTGGACTCTTCATCAACCACTTTGGCACATGCAATTCA
GTGCTTATTATCAACCTGTTGATTGTAATCAATAGCTCCCCCCTTGGGGTCCTGTAAGATAGCAGAGTCAGTGGAAATGC
TGACCTGGGCTGCTTGGTTTTGGCCACTTCTGCAGACTCTGCACAGGTTTTATGCCTATGTATGTTGGAGAGAACTCTCC
TGCTTCACTACAAGAGGCCTTCGGTACCTTCAACTAACTGGGCAGCATCATCAGGATCCTGGTGGCTCAGATATTTGGTC
TGGAGATCATCTTGGGGTCTGAAGAGCTATGGGCTGTGCTGTTGGGCTTCATTCCAGCCATCCTGCAAAGTGCAGCCTTT
CCATTTTGCCCTGAAAGTCCTAGATTCTTGCCCATTAATGGAAAGGAAGAAAATCATGCTAAGCAGATCTTCCAGTAGCT
ACAGAGTACCCAGGATGTGGCTCAGGACATCCAGGGAATGAAAGGTGAGAGTGCTAGGATGGCACAGAAAAAGTCACTCT
GCTAGAGTTCTTCAGGGCACCCAGCTACTAGCAATCCATCTTCATTTCCATCATGCCGCAGCTCTCTCAGCAGCTCTCTG
AGATCAATGCTGTGTTCTATTATTCAACAAGAATTTTCAAGAATGCGGGTGTTAAGGAACCAATCGATGCCACCCTCAGT
GTGAGGGTGGTTATTACTATCTTCACGATAATTTCTGTATTTCTGGTGGAATGAGCAGGAAGGGGGAATCTACATCTGAT
AGGGCTTGGAGGGATGGGTTTTTGCTCTATCCTTATGGCTATTTCTTTTTATTAAAGGATAAGTGTGATACACTGGGCTT
AGACTGTATTGCTGCTATCTTGATCTATGTGGCCTTCTTTGATTTTGGACCAGACACCATTCCCTGGGTTATTGTGGCTG
AGCTCTTCAGCCAGGGACAACACCCCGCTGCAATGGTGGTGGCTGGTTGTTCCAACTGG

Alignment

ORF - retro_ocun_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 69.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VAIFSVG-GMIGSFSVGLF-NRFGRRNSMLIVNLLAVIGGCLMGF-CKISESVEMLI-LGRLVI-GVFCG
          VAIFSV..GMIG.FSVGLF.N.FG..NS.LI.NLL.VI.....G..CKI.ESVEML..LG.LV..G.FC.
Retrocopy VAIFSVK<GMIGLFSVGLFINHFGTCNSVLIINLLIVINSSPLGV>CKIAESVEMLT<LGCLVL<GHFCR

Parental  LCTGFVPMYIGEISPTALRGAFGTLNQLGIVIGILVAQIFGLEIILGSEVLWPVLLGFTIIPAILQSAAL
          LCTGF.PMY.GE.SP..L..AFGT.N.LG..I.ILVAQIFGLEIILGSE.LW.VLLGF..IPAILQSAA.
Retrocopy LCTGFMPMYVGENSPASLQEAFGTFN*LGSIIRILVAQIFGLEIILGSEELWAVLLGF--IPAILQSAAF

Parental  PFCPESPRFLLINKKEEDEAKQILQRLWGTQDVAQDIQEMKEESARMAQ-EKQVTVLELFRAPSYRQPII
          PFCPESPRFL.IN.KEE..AKQI.Q.L..TQDVAQDIQ.MK.ESARMAQ.EK.VT.LE.FRAPSY.Q.I.
Retrocopy PFCPESPRFLPINGKEENHAKQIFQ*LQSTQDVAQDIQGMKGESARMAQ<EK-VTLLEFFRAPSY*QSIF

Parental  ISIVLQLSQQLSGINAVFYYSTGIFKDAGVKEPIYATIGAGVVNTIFTIVSVFLVERAGRRTLHLIGLGG
          ISI..QLSQQLS.INAVFYYST.IFK.AGVKEPI.AT....VV.TIFTI.SVFLVE.AGR..LHLIGLGG
Retrocopy ISIMPQLSQQLSEINAVFYYSTRIFKNAGVKEPIDATLSVRVVITIFTIISVFLVE*AGRGNLHLIGLGG

Parental  MALCSVLMTVS-LLLKDKYDTMSLVCIAAILIYVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNW
          M..CS.LM..S..LLKDK.DT..L.CIAAILIYVAFF..GP..IPW.IVAELFSQG..PAAM.VAGCSNW
Retrocopy MGFCSILMAIS<FLLKDKCDTLGLDCIAAILIYVAFFDFGPDTIPWVIVAELFSQGQHPAAMVVAGCSNW

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	0.00 RPM	120.70 RPM
SRP017611_kidney	0.00 RPM	5.68 RPM
SRP017611_liver	0.00 RPM	2.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_352 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_352 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352 ,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,