RetrogeneDB ID: retro_hvul_6

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:463920060..463922079(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_60699
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_56180
• Aliases: None
• Description: None

Sequence

>retro_hvul_6
ATGGGGATCTCCGTCGCCGTCCCCTCCCTCCTCCTCCTCTCCGCCGCCCTCCTCCTGCCGCCGGCAGCTGCGGGATTCTC
CTTCACCTACAACTTCACCGCCGTCTCGGACTCGGCCCCATCGGGCATCTCCTTCCAGGGCGACGCCTTCTTCAACAAGT
TCATCCGCCTCACCCGCGACGAGCGCGTCGGGCCCCTCACCAGCAGCGCCGGCCGGGCCTTCTTCTCCCGCCCCATCCCA
CTCTTTGACCCTGTCTCCCGCCGCCCCGCCTCGTTCGCCTCCGCCTTCTCCTTCTCCATCTCCGCCCCCGAACCCTCCGC
CGCCTCCGGCGACGGCCTCGCCTTCTTCCTCTCCCCGTTCCCCTCAGTCCTCCCCAACAGATCCGCTGGCGGCCTTCTCG
GGCTCTTCAACTCCTCCGCCCGCAACGGGGGTCGCTCCCTCGTCGCCGTCGAATTCGACACCTACAGGAACGATTGGGAT
CCCAGCGACGACCACGTCGGCATCGACCTCGGGGGCATCGCCTCCGTGGCCACCGCCGACTGGCCGACCAGCATGAAGGA
CGGCCGCACGGCGCACGCGCGCGTCGCGTACGACGCTGAGGCCAAGAACCTCACCGTGGCCCTCTCCTACGGCGACGCTC
CCCCCACGGACGTCCTTCTGTGGTACGCCGTCGATTTGAGGGAACACCTGCCTGACTCCGTGGCCGTTGGCTTCTCCGCC
GCCACTGGCGAGGCCGCCGAGCTGCACAAGGTCCTGTACTGGGATTTCACCTCCAGCGTCGACAGCAAAGAGCAGACGGT
GATGCTGTGGGTGATATTGGGATTGTGCGGATTCCTTGTTGTGCTGGTCGGTGCAGGGGTTGTTTGGTTCGTCAAGGAAT
GGAGGAAGACAGGGGAATGTGTGCCCTATGTCGACATCGACGATGCAATGGGGTACGACGAGCTAACTGACGAGTTCATC
GTGCAGAGCGGGCCAAGACGGTTCCGTTATGCTGAATTGGTGGCGGCAACCAACAATTTCTCCGAGCAGAGGAAGCTCGG
GCAGGGCGGGTTCGGTGCTGTTTACCGGGGGTTCTTGAAGGAGCTCCGTCAGGAGGTGGCCATCAAGAGGGTCTCCAAGG
GGTCGACGCAGGGGCGCAAGGAGTACGCAGCCGAGGTACGCATCATCAGCCAGCTGCGCCACCGGCATTTGGTCCGGCTT
GTCGGGTGGTGCCATGAACACCGTGGTGACTTCTTGCTCGTCTATGAGCTCATGCCCAATGGCAGCGTCGACCAGCACCT
CTACGGCAAAGGCGTGCACCTCACCTGGCCGACACGGTATGACATTGCACTGGGCCTCGCGTCGGCATTGCTCTACCTCC
ACGAGGAGTGCCTTCAGTGCATCGTGCACCGCGACATCAAGCCGAGCAATGTGATGCTGGATGCCACCTTCAGTGCCAAG
CTCGGCGACTTTGGCCTTGCCAAGCTAGTTGAGCATGGCAGCCAGCCCTACACCACCGTCCTGGCTGGCACGTTAGGCTA
CTTGGCGCCAGAGTGCCTGACGACAGGCAAGGCAAGCCGGGAATCGGACGTGTACAGCTTCGGCGTCGTGGCACTGGAGA
TTGCTTGCGGACGACAGCCATCGGAGCCCACGGCGGAGCCGAGCAAGGCAAGGCTGGTGCCGTGGGTGTGGGAGCTTTAT
GGGAAGAAAGCCCTTCTCGAAGCGGCGGACTGGAGGTTGAAGGGGGAGTTTGACGAGAAGCAGATGGAGCATCTGATGGT
GGTCGGACTATGGTGCGCTCATCCGGACTACACGCATAGGCCAAGCATCAGGCAGGCCCTGAATGCCCTGAAATTTGAGG
CGCCATTGCCTGTGCTAGCGCCGAAGATGCCGGTGCCGACGTTCTTCCCTTTGCCTGACTTGGCTGCTCTGGTATCATCA
GTTGGAGGTGCGCAGAACCCAGGCGTTACTGAGTGCGAGTCATCAGGGGCTAATGCTGGCCAACGGTCTTCGGTGAGGGA
TAGACTTCTGGAGCCATGA

Alignment

ORF - retro_hvul_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.57 %
• Parental protein coverage: 66.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLRNVGLPQEAAVGFSASIGDLVEKHQILSWSFQSSMTDSKTKGTSLIAGLVSSGLLILLAIAVWLGYR
          VDLR...LP...AVGFSA..G...E.H..L.W.F.SS..DSK.....L....V..GL...L...V..G..
Retrocopy VDLRE-HLPDSVAVGFSAATGEAAELHKVLYWDFTSSV-DSKEQTVML---WVILGLCGFLVVLVGAGVV

Parental  QYVKRKGKNIHDNIPEDADETPLDDQDMDSELEKGTAPRRFSYSELWRATRGFSDDEKLGEGGFGAVYRG
          ..VK...K......P...............E......PRRF.Y.EL..AT..FS...KLG.GGFGAVYRG
Retrocopy WFVKEWRKT-GECVPYVDIDDAMGYDELTDEFIVQSGPRRFRYAELVAATNNFSEQRKLGQGGFGAVYRG

Parental  FLHDRGLHVAIKRVSKMSSQGRREYIAEVTTIGRLRHRNLVQLVGWCHK-ADELLLIYELMTNGSLDVHL
          FL......VAIKRVSK.S.QGR.EY.AEV..I..LRHR.LV.LVGWCH......LL.YELM.NGS.D.HL
Retrocopy FLKELRQEVAIKRVSKGSTQGRKEYAAEVRIISQLRHRHLVRLVGWCHEHRGDFLLVYELMPNGSVDQHL

Parental  YKSRDILTWPIRYKITLGMGHALMYLHQEWEQCVVHRDIKPSNVMLDSSFDARLGDFGLARLVDHSRGAH
          Y.....LTWP.RY.I.LG...AL.YLH.E..QC.VHRDIKPSNVMLD..F.A.LGDFGLA.LV.H.....
Retrocopy YGKGVHLTWPTRYDIALGLASALLYLHEECLQCIVHRDIKPSNVMLDATFSAKLGDFGLAKLVEHGSQPY

Parental  TTMLAGTKGYMDPQCAVTSRASAETDVYSFGVVLLEIACGRRPVIQELEDESRMVLVEWVWALYGRGALL
          TT.LAGT.GY..P.C..T..AS.E.DVYSFGVV.LEIACGR.P........S...LV.WVW.LYG..ALL
Retrocopy TTVLAGTLGYLAPECLTTGKASRESDVYSFGVVALEIACGRQP-SEPTAEPSKARLVPWVWELYGKKALL

Parental  DAVDARLDGEFDAREMERTLLVGLWCVHPDYGFRPSIRQAMSVLQFEAPLPELPPEMPVALLYVLP
          .A.D.RL.GEFD...ME....VGLWC.HPDY..RPSIRQA...L.FEAPLP.L.P.MPV.....LP
Retrocopy EAADWRLKGEFDEKQMEHLMVVGLWCAHPDYTHRPSIRQALNALKFEAPLPVLAPKMPVPTFFPLP

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_6 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_56180	1 retrocopy	retro_hvul_6 ,