RetrogeneDB ID: retro_hvul_98

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:540716263..540717049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_37295
• Aliases: None
• Description: None

Sequence

>retro_hvul_98
CGCGCCGGGGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTGGACGAGTACACGGTGACGGTGGTGGACGT
GTTCGCGATGCCGCAGAGCGGCACGGGCGTGAGCGTGGAGGCCGTCGACGACGCCTTCCAGACCGGCATGATGGGCATGC
TGCGGCAGACGGGGCGGCCGGAGATGGTGGTGGGCTGGTACCACTCCCACCCGGGCTTCGGCTGCTGGCTCTCGGCCACC
GACATCCAGACGCAGCTCAGCTTCGAGCAGCTCAACCCGCGCGCCGTCGCCGTCGTGCTCGACCCCATACAGAGCGTCAG
GGGCAAGGTGGTCATGGACGCCTTCCGCCTCATCAACCCCACGGCGATCCTCATGCGCCAAGAGCCGCGCCAGACCACCT
CCAACGTCGGCGCCACCGTGCGCCCCTCCCTCGACGCGCGCATCCAAGGCCTCGGCGTGCACTACTACTCGCTCGTCATC
GGCCACCGCCAGAACGAGGTCGAGGAGGGCATGCTCGCCTGCCTCAACCGCAGCCGCTGGTCCCACGGGCTCGTCCTGCC
AAGCTTCGACGACGACGAGAACGAGGCCGCCGTGAGCGGGATCCGGGACCTCGCGGTGCAGTACGACGTGCAGGTCAGGG
AGGAGGACGCGACGCAGCCGGAGAGGCTGGCCGTGGTCAGGGCGGGCAGGCCGGACGCCAAGAAGCAGCTCGGGGAGAGA
GCCGAGGCCGCCATGTCCGGCAACATCGTGCACACGCTCGGCATGATGCTCGACACGGTCGCCTTC

Alignment

ORF - retro_hvul_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.29 %
• Parental protein coverage: 75.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAGVPMEVMGLMLGEFVDDYTVRVVDVFAMPQSGTGVSVEAVDHVFQTNMLDMLKQTGRPEMVVGWYHSH
          RAGVPMEVMGLMLGEFVD.YTV.VVDVFAMPQSGTGVSVEAVD..FQT.M..ML.QTGRPEMVVGWYHSH
Retrocopy RAGVPMEVMGLMLGEFVDEYTVTVVDVFAMPQSGTGVSVEAVDDAFQTGMMGMLRQTGRPEMVVGWYHSH

Parental  PGFGCWLSGVDINTQQSFEALNPRAVAVVIDPIQSVKGKVVIDAFRLINPQTMMLGQEPRQTTSNVGHLN
          PGFGCWLS..DI.TQ.SFE.LNPRAVAVV.DPIQSV.GKVV.DAFRLINP......QEPRQTTSNVG...
Retrocopy PGFGCWLSATDIQTQLSFEQLNPRAVAVVLDPIQSVRGKVVMDAFRLINPTAILMRQEPRQTTSNVGATV

Parental  KPSIQALIHGLNRHYYSIAINYRKNELEEKMLLNLHKKKWTDGLIIKKFDTHSKTNEETVQEMLSLAIKY
          .PS..A.I.GL..HYYS..I..R.NE.EE.ML..L....W..GL....FD.....NE..V.....LA..Y
Retrocopy RPSLDARIQGLGVHYYSLVIGHRQNEVEEGMLACLNRSRWSHGLVLPSFD--DDENEAAVSGIRDLAVQY

Parental  NKAVQEEDELPPEKLAIANVGRQDAKKHLEEHVSNLMSSNIVQTLGTMLDTVVF
          ...V.EED...PE.LA....GR.DAKK.L.E.....MS.NIV.TLG.MLDTV.F
Retrocopy DVQVREEDATQPERLAVVRAGRPDAKKQLGERAEAAMSGNIVHTLGMMLDTVAF

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_98 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_30029	1 retrocopy	retro_atau_45,
Hordeum vulgare	MLOC_37295	1 retrocopy	retro_hvul_98 ,
Oryza barthii	OBART05G14050	1 retrocopy	retro_obar_8,
Oryza glumaepatula	OGLUM05G14910	1 retrocopy	retro_oglu_36,
Oryza nivara	ONIVA05G14600	1 retrocopy	retro_oniv_12,
Oryza punctata	OPUNC05G12230	1 retrocopy	retro_opun_28,
Oryza glaberrima	ORGLA05G0247800	1 retrocopy	retro_ogla_24,
Oryza rufipogon	ORUFI05G15150	1 retrocopy	retro_oruf_24,
Oryza sativa japonica	OS05G0371200	1 retrocopy	retro_osat_40,