RetrogeneDB ID: retro_hvul_66

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:537116452..537118117(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_58062
• Aliases: None
• Description: None

Sequence

>retro_hvul_66
ACCATGGACGGGACGATGGACGTGTCCGGCAAGCCGGCGGTGAGGAGCAAGACTGGCGGGTGGAGGGCGTGCCCCTTCAT
CCTGGGCAACGAGTGCTGCGAGCGGCTCGCCTACTACGGCATGAGCTCCAACCTCGTCAACTACATGATCGACCGCCTCC
ACCAGGGCAACGCCGCCGCCGCCACCAACGTCAACAACTGGTCCGGCACCTGCTACGTCATGCCCCTCCTCGGCGCCTTC
CTGGCCGACGCCTATCTTGGTAGGTTCCGCACCATCGCCGCCTTCATGGCACTCTACATCGCCGGCCTCGCCCTCCTCAC
CCTCTCCGCCACCGTCCCCGCCCTCCGCCCGCCAGACTGCGCCGGCTGCCCGCCCTCCGCGGGACAGAACGCCGCCTTCT
TCACCGCGCTCTACCTCATCGCCGTCGGCACGGGCGGGATCAAGCCCTGCGTCTCCTCCTTCGGCGCCGACCAGTTCGAC
GACGCCGACCCGCGCGAGATGCGCAGCAAGAGCTCCTTCTTCAACTGGTTCTACATGTCCATCAACGTCGGCGCCCTCGT
CGCCTCCTCGGTGCTCGTCTGGGTCCAGATGAACGTCGGATGGGGCTGGGGCTTTGGGATCCCCGCCGCCGCCATGGCCG
TCGCCGTCGCCAGCTTCCTCATGGGCAGCAGGCTCTACCGGTACCAGAGGCCCGGGGGCAGCCCGCTCACCAGGATGCTG
CAGGTGCTGGTCGCCGCCTGCAGGAAGTCGCACGTGCCGCTCCCCGCCGACGCCTCGCTGCTGCACGAGGTGGCGTCGCC
GGACGGCAAGGCGGCCATCGAGGGCAGCAGGAGGCTGGAGCACACTGAGCAGCTGAGGTGCCTCGACAGGGCGGCGGTGG
TTGTGGATCCCGGCGAATCCGACGACCCGTGGAGGCTTTGCACGGTGACGCAGGTGGAGGAGCTCAAGAGCATGGTGCGG
CTGCTCCCGGTGTGGGCGAGCGGCATCGTCATGTCGGCGGTCTACAGCCAGATGAGCACCATGTTCGTGCTCCAGGGAAA
CACGCTGGACCCGCGCATGGGCGCCACCTTCAAGATCCCCGCCGCCTCCCTCTCCATCTTCGACACCATCGCCGTCATCG
TGTGGGCGCCGGCCTACGACCGCCTCATCGTGCCCGCCGCGCGCCGGGTCACGGGCCACCCGCGAGGCTTCACGCAGCTC
CAGCGCATGGGCATCGGGCTCGTCATATCCATATTCTCCATGGTGGCGGCCGGGGTGCTGGAGGTGGCCAGGCTCCGCGT
GGCCGCCGGCCACGGCATGCTCGACTCCAAGGACTACCTGCCCATGTCCATCTTCTGGCAGGTGCCGCAGTACTTGATCG
TGGGCGCCGCCGAGGTCTTCACCTTCGTGGGGCAGATCGAGTTCTTCTACGACCAGTCGCCGGACGCCATGAGGAGCATG
GGCTCGGCGCTCTCGCTCACGTCCAACGCGCTGGGAAATTACCTGAGCACGCTGCTCGTGGTGATCGTGACGGCCGTCTC
GACGAGGAACGGAGGCATCGGGTGGATCCCGGACAACCTCAACCGGGGGCACCTCGACTACTTCTACTGGGTGCTGGCCG
TGCTCAGCGCCCTCAACTTCATCGTCTACCTCTGGATTGCAAAGTGGTACAAGTACAAGCAGGCC

Alignment

ORF - retro_hvul_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.03 %
• Parental protein coverage: 95.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGDGSVDFSGNPVVKEKTGRWKACPFILGNECCERLAYYGISTNLVTYLTKKLHDGNSSAARNVTTWQGT
          T.DG..D.SG.P.V..KTG.W.ACPFILGNECCERLAYYG.S.NLV.Y....LH.GN..AA.NV..W.GT
Retrocopy TMDGTMDVSGKPAVRSKTGGWRACPFILGNECCERLAYYGMSSNLVNYMIDRLHQGNAAAATNVNNWSGT

Parental  CYLTPLIGAILADAYWGRYWTIATFSTIYFIGMSVLTLSASVPMLMPPSCEGAICPEASPLQYTVFFLGL
          CY..PL.GA.LADAY.GR..TIA.F...Y..G...LTLSA.VP.L.PP.C.G..CP.....Q...FF..L
Retrocopy CYVMPLLGAFLADAYLGRFRTIAAFMALYIAGLALLTLSATVPALRPPDCAG--CPPSAG-QNAAFFTAL

Parental  YLIALGTGGIKPCVSSFGADQFDDTDPAERIQKGSFFNWFYFSINIGALISSSFLVWVQDNLGWGLGFGI
          YLIA.GTGGIKPCVSSFGADQFDD.DP.E...K.SFFNWFY.SIN.GAL..SS.LVWVQ.N.GWG.GFGI
Retrocopy YLIAVGTGGIKPCVSSFGADQFDDADPREMRSKSSFFNWFYMSINVGALVASSVLVWVQMNVGWGWGFGI

Parental  PTVFMGLAIISFFAGTSLYRFQKPGGSPITRVCQVVAATLRKWNAHVPEDSALLYEL--PDGVSAIEGSR
          P...M..A..SF..G..LYR.Q.PGGSP.TR..QV..A..RK.....P.D..LL.E...PDG..AIEGSR
Retrocopy PAAAMAVAVASFLMGSRLYRYQRPGGSPLTRMLQVLVAACRKSHVPLPADASLLHEVASPDGKAAIEGSR

Parental  QLEHTDELRCLDKAATITDLDVKEDSFNNPWRVCTVTQVEELKILVRMFPVWATTIVFSAVYAQMSTMFV
          .LEHT..LRCLD.AA...D.....D....PWR.CTVTQVEELK..VR..PVWA..IV.SAVY.QMSTMFV
Retrocopy RLEHTEQLRCLDRAAVVVDPGESDD----PWRLCTVTQVEELKSMVRLLPVWASGIVMSAVYSQMSTMFV

Parental  EQGMVLDPTIGS-FKIPPASLSTFDVVSVIIWVPIYDSILVPIARRFTGKERGFSELQRMGIGLIISILA
          .QG..LDP..G..FKIP.ASLS.FD...VI.W.P.YD...VP.ARR.TG..RGF..LQRMGIGL.ISI..
Retrocopy LQGNTLDPRMGATFKIPAASLSIFDTIAVIVWAPAYDRLIVPAARRVTGHPRGFTQLQRMGIGLVISIFS

Parental  MSAAAVLEIKRLAIAREAHLVDQNVPVPLSILWQIPQYFLVGASEVFTFIGALEFFYDQSPDAMRSLCSA
          M.AA.VLE..RL..A......D.....P.SI.WQ.PQY..VGA.EVFTF.G..EFFYDQSPDAMRS..SA
Retrocopy MVAAGVLEVARLRVAAGHGMLDSKDYLPMSIFWQVPQYLIVGAAEVFTFVGQIEFFYDQSPDAMRSMGSA

Parental  LQLITTALGNYLSAFILTMVAYFTTRGGRPGWIPDNLNEGRLDNFFWLLAGLSFLNFLVYVVCANRFKSK
          L.L...ALGNYLS......V....TR.G..GWIPDNLN.G.LD.F.W.LA.LS.LNF.VY...A...K.K
Retrocopy LSLTSNALGNYLSTLLVVIVTAVSTRNGGIGWIPDNLNRGHLDYFYWVLAVLSALNFIVYLWIAKWYKYK

Parental  KA
          .A
Retrocopy QA

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_66 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009904	1 retrocopy	retro_oind_36,
Hordeum vulgare	MLOC_58062	1 retrocopy	retro_hvul_66 ,
Oryza glumaepatula	OGLUM02G34910	1 retrocopy	retro_oglu_17,
Oryza glaberrima	ORGLA03G0409900	1 retrocopy	retro_ogla_29,
Oryza rufipogon	ORUFI03G33580	1 retrocopy	retro_oruf_5,
Oryza sativa japonica	OS03G0719900	1 retrocopy	retro_osat_25,
Triticum aestivum	Traes_4AL_59D5504B1	1 retrocopy	retro_taes_96,