RetrogeneDB ID: retro_btau_36

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:46287375..46288566(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047652
• Aliases: RBMXL2, HNRNPG-T, RBMX
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RBMX
• Ensembl ID: ENSBTAG00000013308
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein G [Source:RefSeq peptide;Acc:NP_001165510]

Sequence

>retro_btau_36
ATGGTGGAAGCGGATCGCCCGGGGAAGCTCTTCATTGGAGGACTCAACCTCGAAACTGACGAGAAATCCCTCGAGGCTAC
GTTTGGCAAGTATGGCCGCATTTCCGAGGTGCTGTTGATGAAAGATCGAGAAACCAACAAGTCCAGGGGCTTCGCCTTCA
TCACCTTCGAAAGTCCGGCAGACGCGAAGGCCGCCGTGAGAGACATGAACGGCAAGTCCCTGGATGGTAAGGCCATCAAG
GTGGCCCAGGCCACCAAACCAGCTTTCGAGAGCGGCCGGCGGGGCCCACCCCTGTCCCGCAGCCGGGGCCGCTCGAGGGG
CCTGCGCGGGGCCCGCGGCGGCGGTCCGCGGCGCCCCCCGTCCCGCGGAGGGCCTGCGGATGATGGCGGCTACGCGGGCG
ACTTCGACCTGCGGCCCTCCCGGGCCCCGCTACCCATGAAGCGCGGGCCGCCACCACCACGGAGGGCCGGCCCGCCCCCC
AAGAGGGCCGCGCCGTCGGGCCCTGCGCGCAGCGGCAGCGGTGGTGGAATGCGCGGGCGGGCTCCGGCCGCGCGAGGTCG
AGACGGCTATGAGGGCCCGCCGCGCCGAGATCCGCCGCCCCCGCGCCGGGATCCCTACCTGGGTTCCCGGGAGGGGGGCT
ACTCTCCCCGAGACGGCTACTCCAGCCGCGACTACTCGAGCGCCCGCGACGCCCGGGATTTTGCCCCCTCGCCCAGAGAG
TATACCTACCGCGACTACGGCCACTCCAGCGCCCGGGATGAGTGTCCATCGAGAGGCTACGGCGACCGAGACGGCTACGG
GGGGCGCGACCGCGACTACGCGGATCACCCTAGCGGAGGCTCCTACCGAGATCCCTTCGAGAGCTACGGGGACCCGCGCA
GCGCCGCCCCCGCGCGTGGGCCCCCTCCATCTTATGGTGGCGGCGGCGGCCGCTATGAGGAGTACCGCGGCTGCTCGCCC
GACGCCTATGGCGGCGGCCGCGACGGTTATGCTGGGGGCCGGAGCGAGCGCTACTCGGGGGGCCGCGACCGGGTAGGCAG
AGCGGATCGCGGGCTGCCGCAGTCCGTGGAGAGGGGGTGTCCGCCCCCGCGCGAGTCTTACAGCCGGTCGGGCCGCAAGG
TCCCCCGAGGCGGAGGCCGCCTGGGGAGCCGCTCGGAGAGAGGAGGAGGAGGAGGCCGGAGCAGATACTAA

Alignment

ORF - retro_btau_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
          MVEADRPGKLFIGGLN.ET.EK.LEA.FGKYGRI.EVLLMKDRETNKSRGFAF.TFESPADAK.A.RDMN
Retrocopy MVEADRPGKLFIGGLNLETDEKSLEATFGKYGRISEVLLMKDRETNKSRGFAFITFESPADAKAAVRDMN

Parental  GKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSHGGHMDDGGYSMNFNM
          GKSLDGKAIKV.QATKP.FESGRRG.PP..RSRG..RGLRG.RG..GG.R.PPS.GG..DDGGY...F..
Retrocopy GKSLDGKAIKVAQATKPAFESGRRG-PPLSRSRGRSRGLRGARG--GGPRRPPSRGGPADDGGYAGDFDL

Parental  SSSRGPLPVKRG-PPPRSGGPPPKRSAPSGPVRSSS--GMGGRAPVSRGRDSYGGPPRREPLPSRRDVYL
          ..SR.PLP.KRG.PPPR..GPPPKR.APSGP.RS.S..GM.GRAP..RGRD.Y.GPPRR.P.P.RRD.YL
Retrocopy RPSRAPLPMKRGPPPPRRAGPPPKRAAPSGPARSGSGGGMRGRAPAARGRDGYEGPPRRDPPPPRRDPYL

Parental  SPRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGY-GRDRDYSDHP
          ..R..GYS..D.YSSRDY.S.RD.RD.AP.PR.YTYRDYGHSS.RD..PSRGY.DRDGY.GRDRDY.DHP
Retrocopy GSREGGYSPRDGYSSRDYSSARDARDFAPSPREYTYRDYGHSSARDECPSRGYGDRDGYGGRDRDYADHP

Parental  SGGSYRDSYESYGNSRSAPPTRGPPPSY-GGSSRYDDY-SSSRDGYGGSRDSYSSSRSDLYSSGRDRVGR
          SGGSYRD..ESYG..RSA.P.RGPPPSY.GG..RY..Y...S.D.YGG.RD.Y...RS..YS.GRDRVGR
Retrocopy SGGSYRDPFESYGDPRSAAPARGPPPSYGGGGGRYEEYRGCSPDAYGGGRDGYAGGRSERYSGGRDRVGR

Parental  QERGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDR--GGGRSRY
          ..RGLP.S.ERG.PPPR.SYS.S.R..PRGGGR.GSRS.R..GGGRSRY
Retrocopy ADRGLPQSVERGCPPPRESYSRSGRKVPRGGGRLGSRSERGGGGGRSRY

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
ERP005899_liver	0.00 RPM	37.49 RPM
ERP005899_muscle	0.00 RPM	105.21 RPM
SRP017611_brain	0.00 RPM	58.06 RPM
SRP017611_kidney	0.00 RPM	82.92 RPM
SRP017611_liver	0.00 RPM	40.09 RPM
SRP030211_testis	79.11 RPM	14.93 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_36 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_36 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_91
Mus musculus	retro_mmus_170

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001697	2 retrocopies	retro_btau_1245, retro_btau_850,
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36 ,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,