RetrogeneDB ID: retro_hvul_69

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:43100804..43101869(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_5612
• Aliases: None
• Description: None

Sequence

>retro_hvul_69
GATCCTAATGGCGTGATGTACTACAAGGGCCTGTACCACCTCTTCTACCAGTACAACCCCAAGGCGGCCGTCTGGGGCAA
CATCGTCTGGGCGCACGCCGTGTCCACGGACCTGGTCAACTGGGTCATGCTCCAGCCGGCCATCTACCCCTCGGCGCCCT
TCGACGTTAACGGCTGCTGGTCCGGCTCCGCCACCGTCCTGCCCGACGGCACGCCCGCCATCATGTACACCGGCATCGAC
GGCGACGGCCGGCAGGTGCAGAACGTTGCCTACCCCAAGGACCTCTCGGATCCCTACCTCCGGGAGTGGGTCAAGCCGGA
CTACAACCCCGTCATCGCGCCCGGCGCCGGGGTGAACGCCACCGCGTTCCGTGACCCGACGACGGCGTGGCGGGGACCCG
ACGGGCTCTGGCGCCTGGTCGTCGGAACCAAGGACAACCACCGGGGCCTCGCCGTGCTCTACCGCAGCCGGGACTTCCGG
CGCTGGGTGCCGGTGCGCCGAGCGCTGCACCACGGCGACACCGGCATGTGGGAGTGCCCGGACTTCTACCCCGTCACCCC
CCACGGCGTCCCCGGCGATGTCAAGCACGTTCTCAAGGTGAGCCTCGACCTGACCCGCTTCGAGTACTACACCTTCGGCG
CGTACGACCACGCCACCGAGACGTACGTGCCGGACGCGGCGCTCCCTGACGGCAACGACGGGCTCCGCTACGACTACGGC
AACTTCTACGCGTCCAAGACGTTCCTCGACCCGGCGAAGCACCGCCGCGTGCTGTGGGGTTGGGCCAACGAGTCGGACTC
CACAGCCGACGACGTCAGGAAGGGCTGGGCCGGCGTGCAGGCCATCCCCAGGAAGATCTGGCTGTCGGCGGACGGCAAGC
AGCTCATGCAATGGCCGGTCACCGAGGTCGAGTCCCTCCGCGGCAACCACGTTAACATCACCGACAGGCTCGTCAAGGGC
GGGGACTACTTCGAGGTCCTCGGGCTCACGACGCCGGCGCAGGCCGACGTCGAGGTGTCGTTCGCGGCGATGGACCTGGA
CAAGGCCGAGCAGTTCGACCCAGCA

Alignment

ORF - retro_hvul_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 62.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPNGPLYYKGWYHLFYQYNPRGADWVNTLWAHSVSRDLINWNLLGLALEPSIRPDKYGVWSGSATILLDG
          DPNG..YYKG.YHLFYQYNP..A.W.N..WAH.VS.DL.NW..L..A..PS...D..G.WSGSAT.L.DG
Retrocopy DPNGVMYYKGLYHLFYQYNPKAAVWGNIVWAHAVSTDLVNWVMLQPAIYPSAPFDVNGCWSGSATVLPDG

Parental  TPVLVYTGINRQDIPYQVQNIAIPKNKSDPLLREWVKPDYNPIIVPESGMNVTQFRDPSTAWH-IDGQWR
          TP...YTGI.......QVQN.A.PK..SDP.LREWVKPDYNP.I.P..G.N.T.FRDP.TAW...DG.WR
Retrocopy TPAIMYTGIDGDG--RQVQNVAYPKDLSDPYLREWVKPDYNPVIAPGAGVNATAFRDPTTAWRGPDGLWR

Parental  ILVGGEKGSQGQAYVYRSTDFKHWVRAKHPLHSAINGMWECLDFFPVLMQGKKGLDTYEHSARVKYVLKS
          ..VG......G.A..YRS.DF..WV.....LH....GMWEC.DF.PV...G..G.....H...V...L..
Retrocopy LVVGTKDNHRGLAVLYRSRDFRRWVPVRRALHHGDTGMWECPDFYPVTPHGVPG--DVKHVLKVSLDL-T

Parental  SLEKARYDYYTIGTYDNRTESYVPDDLNGDYHRLRYDYGKFYASKTFFDPAKQSRVLVGWANESDTVPDD
          ..E......Y...T.........PD...G....LRYDYG.FYASKTF.DPAK..RVL.GWANESD...DD
Retrocopy RFEYYTFGAYDHATETYVPDAALPDGNDG----LRYDYGNFYASKTFLDPAKHRRVLWGWANESDSTADD

Parental  IAKGWSGIHAIPRKIWLDPGGKQLVQWPIEEVEQLRRKSVSVTNKVVKPGDHFEVKGLET-YQADVEVTF
          ..KGW.G..AIPRKIWL...GKQL.QWP..EVE.LR...V..T...VK.GD.FEV.GL.T..QADVEV.F
Retrocopy VRKGWAGVQAIPRKIWLSADGKQLMQWPVTEVESLRGNHVNITDRLVKGGDYFEVLGLTTPAQADVEVSF

Parental  KIRSLERAEPFDQA
          ....L..AE.FD.A
Retrocopy AAMDLDKAEQFDPA

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_69 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_5612	1 retrocopy	retro_hvul_69 ,