RetrogeneDB ID: retro_hvul_14

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:288582726..288585918(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_10168
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_5589
• Aliases: None
• Description: None

Sequence

>retro_hvul_14
ATGGCGAGCGAGGAGCGTCAGCTCAAGACGCGGGTGTCGGACCGTCTGATGGCGCTCGTGGGCTACTCCGAGGTCATGGT
GGTGCGCCTGGTGCTCCGCCTCGCGCGGGAGAGCGCGTCGGCGGCCGACCTCGCGGCGCGCCTCGTCGACCTCGCCGGCC
TCCCCTCCTCCGCCGACACCGTCGCGTTCGCGGAGGACGTGCACGCCATGTTCCCCCGCAAGGGCTCCCGCGTCAGCGAG
TACCGGAAACAGGTGCAGGAGGCGGCGGCGTTCGCCAAGAAGCAGAGCGCCTTCAAGCTGCTCGACGATGAAGACGATCA
CGCTCAAGATGCCGGCGCCATCGCCACGGCCACTGCGTCGTCCTCTAACACCAGCGGCAAGAAGCGCTTCAGGCAGAATG
CCGCGAGCCCAGGGGATGACGACGAGGAGGAGGAGGGGACTGTAATGCGCGATTCAGGGCGGAAAGTGCGAGCGCAGCGT
GCTCCCGCGGAGGACGGCGACGGTTCTGATGGGGAGGAACTGGAAGAGATGGACCGTGATCAGATCGAGAAGGCTCAGCT
CGATCGGCACATCAGAGAACGCGACGCAGCCAGCACTAGGAAACTGACGGATCGGAAGCCGACCAAGCGAGAGCAGGGCG
AGCTTGGCCGGCGGTCCGAAGCGTTGGACAGGGGCGACACCTCGGAGCTCAGGACGGCCTCGCGGCAAGCGTACCTGGAA
AAGCGGAAGAAGATGAAGGTGGAGGAGATGCAAGACGAGATTATCGACAACGAGTTTATCTTCGACGGCGTCAAGATGAC
GAACGCCGAAGAGATGGAATTAAGGCGAAAGAAGGAAATCTACGACCTTGTCAAGGTTAGCGTCGGAAAGGACGCCGACG
CCGACGCCGGCGACTACTACAGGATGCCCGACGCATACGACGCCGCAGCAAACGTGGATCAGGCGAAACGGTTTGCCGTT
CAGAGGCAGCGGTACGATGACCCCGAGGCGGCGGCGAGAGACGGCAAGAGGAGCAATTTCTTCTCGGAGCAGGAGGCCTG
GGAAGAGCAGCAGATAAGGAAGTCTCGGCTACACTTCGGATCAGATGATGGTGGCCGGGCCGGCGGCGGCTACGAGCTCG
TCTTGGAAGGCGTGGTCGACTTCGTCAAGTCGACGGTGCAGGCCGGCGCCGAGCCGGACGGCGAGATGGACGAACTTGCC
GAGGCAATCGATGCCAAGGTGACATTGCAGAGGGAGCTGCAGGACGAGAGGAAGAATCTGCCCGTGTACAAGTTCAAGGA
CGATCTTCTCAAGGCCATCGACAAGTACCAGGTGCTGATCATCGTCGGAGAGACCGGCTCCGGCAAGACCACGCAGATAC
CGCAGTACCTCCACGAGGCCGGGTACACGGCCAAGGGGAAGAAGATCGCGTGCACGCAGCCGCGTCGCGTCGCTGCGATG
AGCGTGGCGGCGAGGGTGGCGCAGGAGATGGGCGTCAAGCTCGGGCACGAGGTCGGCTACTCGATCAGGTTCGAGGACTG
CACCTCAGACAAGACGGTGATCAAGTACATGACGGACGGGATGCTCCTGCGGGAGTTCCTCGGCGAGCCGGACCTGGCGA
GCTACAGCGTGGTGATGGTGGACGAGGCGCACGAGCGCACGCTCTCCACCGACATCCTCTTCGGCCTGGTCAAGGACATT
GCGCGCTTCCGGCCGGACGTGAAGCTGCTCATCTCGAGCGCGACGCTCAACGCCGAGAAGTTCAGCGACTTCTTCGACGA
GGCCCCGATCTTCAAGATCCCCGGGAGACGGTACAAGGTGGACATCCACTACACGACGGCGCCGGAGGCGGATTACATCG
CCGCCGCCGTCGTCACGGTCCTGCAGCTGCACGTCACCCAGCCCGCCGGCGACATCCTGCTGTTCCTCACGGGGCAGGAG
GAGATCGAGACGGTGGAAGAGATGCTGAAGCAGAAGATGAGGACATTTGGCGGCAAGATGGCAGAGCTGGTGATCTGCCC
GATCTACGCGAACCTGCCCACGGAGCTCCAGGCCAAGATCTTCGAGCCGACGCCGGAGGGCTCCCGCAAGGTGGTTGTGG
CCACCAACATCGCCGAGACGTCGCTGACCATCGACGGGATCAAGTACGTGATCGACCCGGGGTTCTGCAAGCTCAAGTCG
TACAACCCGCGCACGGGCATGGAGTCGCTGCGGGTTGAGCCCATCTCCAAGGCGTCGGCGGACCAGCGTGCCGGCCGGTC
GGGGCGGACAGGACCCGGCAAGTGCTTCCGCCTCTTCACGGAGTACAACTTCAGGAACGACCTGGACGACGACACGGTCC
CGGAGATCCAGAGGAGCAACCTGGCCAACGTGGTGCTGAGGCTCAAGGCGCTGGGCATCAACGACCTGGTGAGCTTCGAC
TTCATGGACCCACCGGCGTCGGAGGCGCTGCTCAAGGCCCTGGAGGAGCTCTTCGCCCTCGGGGCGCTCAACAGCCGTGG
CGAGCTCACCAAGACCGGGAGGAGGATGGCCGAATTCCCGCTGGACCCCATGCTCTCCAAGGCCATCGTGGCGTCGGAGA
AGTACAAGTGCTCCGAGGAGGTGGTGACCATCGCGGCCATGCTATCTGCCGGGAACGCCGTCTTCTACCGGCCCAAAGAC
AAGCTGGTGCACGCCGACACGGCGCGGCAGGCCTTCCACGCGGGCAACGTCGGTGACCACGTGGCGCTGCTCAACGTGTA
CAACGCGTGGAAGGAGTCGGGCTACTCGTCGCAATGGTGCCGCGAGAACTTCGTGCAGCCGCGCACCATGAAGCGCGCGC
GGGATGTGCGGGACCAGCTGGAGGCGCTGCTGGAGCGGGTGGAGATCGAGCACTGCTCCGGCGTCGGCGACCTCGGCGCG
ATAACGAAGGCGGTCACGGCGGGCTACTTCCGCAACGCGGCGCGGAGGCAGAAGGACGGGTCGTACCGTGCCGTCAAGAG
CCGGCAGACGGTGTTCGTGCACCCGAGCTCCGGGATGGCGGAGGTGACGCCGTCATGGGTGGTGTACCACGAGCTGGTGC
TGACCACCAAGGAGTACATGCGGCAGGTGACGGAGCTCAAGCCGGAGTGGCTGCTGGAGATCGCGCCGCACTATTACCAA
CGCAGGGACATCGACGGGCACGAGCCAAAGAAGATGGCCAAGGGCAAAGGTCCAGCGCCGGCGCCGCTGTAG

Alignment

ORF - retro_hvul_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 95.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASDKQLRDWVSDKLMSIQGFSTSVLVHYVIGLAKDCSSAGDLVGKLVDY-GFSSSAETTSFAADIYAKVP
          ....QL...VSD.LM...G.S....V..V..LA....SA.DL...LVD..G..SSA.T..FA.D..A..P
Retrocopy SEERQLKTRVSDRLMALVGYSEVMVVRLVLRLARESASAADLAARLVDLAGLPSSADTVAFAEDVHAMFP

Parental  RKGKSISNYQKQERDAAKLVKKQSTYKLLADEDDDEIDNHTTSSASASSKS---RKHFRRKTQDQ-DDGK
          RKG...S.Y.KQ...AA...KKQS..KLL.DEDD...D......A.ASS......K.FR.......DD..
Retrocopy RKGSRVSEYRKQVQEAAAFAKKQSAFKLLDDEDDHAQDAGAIATATASSSNTSGKKRFRQNAASPGDDDE

Parental  DDDETAAHISERSVRRRTEEVDDEDGNDTLDEEQEILRDQQERAQLEKNMRERDAVHTRKLMERQLSKEE
          ....T....S.R.VR.......D.DG.D...E..E..RDQ.E.AQL....RERDA..TRKL..R...K.E
Retrocopy EEEGTVMRDSGRKVRAQRAPAEDGDGSDG-EELEEMDRDQIEKAQLDRHIRERDAASTRKLTDRKPTKRE

Parental  QEELTRRSQALEKNDTSDLRDFSRQAYLQKRRDKKIDEIRDEILDHEYLFQDVTLTEAEKNDFRYKKKIF
          Q.EL.RRS.AL...DTS.LR..SRQAYL.KR...K..E..DEI.D.E..F..V..T.AE....R.KK.I.
Retrocopy QGELGRRSEALDRGDTSELRTASRQAYLEKRKKMKVEEMQDEIIDNEFIFDGVKMTNAEEMELRRKKEIY

Parental  DLVKQHV---ESADDVAEYKMPEAYDMGEGVNQEKRFSVAMQRYKDPE--AKD--KMNPFAEQEAWEEHQ
          DLVK..V.....AD....Y.MP.AYD....V.Q.KRF.V..QRY.DPE..A.D....N.F.EQEAWEE.Q
Retrocopy DLVKVSVGKDADADAGDYYRMPDAYDAAANVDQAKRFAVQRQRYDDPEAAARDGKRSNFFSEQEAWEEQQ

Parental  IGKSKLEFGSKDRKRSSNEYQYVFDDQIDFVKSSVIEGTQFEDDSDQ--ETIDAKDILKRELQDERKTLP
          I.KS.L.FGS.D..R....Y..V.....DFVKS.V..G.......D...E.IDAK..L.RELQDERK.LP
Retrocopy IRKSRLHFGSDDGGRAGGGYELVLEGVVDFVKSTVQAGAEPDGEMDELAEAIDAKVTLQRELQDERKNLP

Parental  IYKFRDDLLKAVDEYQVIVIVGETGSGKTTQIPQYLHEAGYTARGK-VACTQPRRVAAMSVAARVSQEMG
          .YKF.DDLLKA.D.YQV..IVGETGSGKTTQIPQYLHEAGYTA.GK..ACTQPRRVAAMSVAARV.QEMG
Retrocopy VYKFKDDLLKAIDKYQVLIIVGETGSGKTTQIPQYLHEAGYTAKGKKIACTQPRRVAAMSVAARVAQEMG

Parental  VKLGHEVGYSIRFEDCTSEKTMIKYMTDGMLLREFLGEPDLAGYSVVMVDEAHERTLSTDILFGLVKDIA
          VKLGHEVGYSIRFEDCTS.KT.IKYMTDGMLLREFLGEPDLA.YSVVMVDEAHERTLSTDILFGLVKDIA
Retrocopy VKLGHEVGYSIRFEDCTSDKTVIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVKDIA

Parental  RFRPDLKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTKAPEADYIDAAIVTILQIHVTQPPGD
          RFRPD.KLLISSATL.AEKFSD.FD.APIFKIPGRRY.V..HYT.APEADYI.AA.VT.LQ.HVTQP.GD
Retrocopy RFRPDVKLLISSATLNAEKFSDFFDEAPIFKIPGRRYKVDIHYTTAPEADYIAAAVVTVLQLHVTQPAGD

Parental  ILVFLTGQEEIETVDEILKHKTRGLGTKIPELNICPIYANLPTELQAKIFETTPEGSRKVVLATNIAETS
          IL.FLTGQEEIETV.E.LK.K.R..G.K..EL.ICPIYANLPTELQAKIFE.TPEGSRKVV.ATNIAETS
Retrocopy ILLFLTGQEEIETVEEMLKQKMRTFGGKMAELVICPIYANLPTELQAKIFEPTPEGSRKVVVATNIAETS

Parental  LTIDGIKYVIDPGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMHDLEDN
          LTIDGIKYVIDPGFCK.KSYNPRTGMESL...PISKASA.QRAGRSGRTGPGKCFRL.T.YN...DL.D.
Retrocopy LTIDGIKYVIDPGFCKLKSYNPRTGMESLRVEPISKASADQRAGRSGRTGPGKCFRLFTEYNFRNDLDDD

Parental  TVPEIQRTNLANVVLTLKSLGIHDLVNFDFMDPPPSEALLKALEQLFALSALNSRGELTKTGRRMAEFPL
          TVPEIQR.NLANVVL.LK.LGI.DLV.FDFMDPP.SEALLKALE.LFAL.ALNSRGELTKTGRRMAEFPL
Retrocopy TVPEIQRSNLANVVLRLKALGINDLVSFDFMDPPASEALLKALEELFALGALNSRGELTKTGRRMAEFPL

Parental  DPMLSKMIVASEKYKCSDEVMSIASMLSIGNSIFYRPKDKQVHADNARLNFHTGNVGDHIALLNVYNSWR
          DPMLSK.IVASEKYKCS.EV..IA.MLS.GN..FYRPKDK.VHAD.AR..FH.GNVGDH.ALLNVYN.W.
Retrocopy DPMLSKAIVASEKYKCSEEVVTIAAMLSAGNAVFYRPKDKLVHADTARQAFHAGNVGDHVALLNVYNAWK

Parental  ETDFSTQWCYENYIQ
          E...S.QWC.EN..Q
Retrocopy ESGYSSQWCRENFVQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq

Hordeum vulgare was not studied using ChIP-Seq data.

EST

Hordeum vulgare was not studied using EST data.

TSS

Hordeum vulgare was not studied using FANTOM5 data.

Lab

retro_hvul_14 was not experimentally validated.

Homology

Retrocopy orthology:

Hordeum vulgare does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14 ,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,