RetrogeneDB ID: retro_hvul_22

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:442958653..442959373(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_39202
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_12641
• Aliases: None
• Description: None

Sequence

>retro_hvul_22
ATGAAGGCCGGGCCATCACCGCCGGCCAGCACCAGCAGGGCGGCGGGCGCGCGGACGCTGGTGGTGCACGTGCTGGCGGT
GGTGGCCACGGTGCTGGTGCTGCTCTGGTGCATCGGTTTCCGCGGCGGCCTCGCCTTCCGCTCCAGCAACAAGCAACAGA
TCTTCAACGTCCCCCCGCCGCTCATGCTCATCGGCCTCGTCGTCATCGCCGGGGAGGCCATCCTCGCCTACCGCACCTTC
CCGGCCTCTGTCAGCCGGGACGCCAGGAAGAAGGCGCACTTGGCGCTGCACGCCGCGGGGCTCGCCGTCGGCCTCGTCGG
CGTCTACGCGGTCTTCAAGTTCCACGCCGAGGCGGACATCCCCAACCTCTACTCGCTGCACGCCTGGATCGGCATCGCCA
CAATCACGCTCTACGCGCTCCAGTGGCTCGCCGGCTTCCTCGCCTTCTTCTTCCCCGGCGCCGCGCCGGAGACCAGGCGG
TCCGCGGTGCCGTGGCACGCCGTGCTGGGGCTCCTCGTCTTCGCGCTCGCCGTGGGCAACGCGCAGCTCGGCTTCCTCGA
AAAGCTCACCTTCCTGCAGTCCCCGCCCGCGCGCCTCGTCGGCAAGTACGGCGCCGAGGCGCTGCTCGTCAACTTCACCG
CCGTCATCGTGCTCCTCCTCGGTATCGCCGTCGTGATCGCCACCGTCAACGCCGACGCCACCAGATACACCGCCATGTGA

Alignment

ORF - retro_hvul_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.02 %
• Parental protein coverage: 89.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TYAAHALAAAAAAMVLVWCIHFRGGLAFEAANKNLIFNVHPVLMLIGFIILGSEAIMVYKVFPG-LNHDT
          T...H.LA..A...VL.WCI.FRGGLAF...NK..IFNV.P.LMLIG......EAI..Y..FP.....D.
Retrocopy TLVVHVLAVVATVLVLLWCIGFRGGLAFRSSNKQQIFNVPPPLMLIGLVVIAGEAILAYRTFPASVSRDA

Parental  AKLTHLILHAIAIVLGAVGIYCAFKFHNDSGIANLYSLHSWLGIGAISLYGIQWIFGFVTFFFPGAAPDV
          .K..HL.LHA.....G.VG.Y..FKFH....I.NLYSLH.W.GI..I.LY..QW..GF..FFFPGAAP..
Retrocopy RKKAHLALHAAGLAVGLVGVYAVFKFHAEADIPNLYSLHAWIGIATITLYALQWLAGFLAFFFPGAAPET

Parental  RRGALPWHALFGLFVYVLTLATAELGFLEKMTFLQSSG---LDKYGPEALLVNFTALVVVLLGAAVVVAA
          RR.A.PWHA..GL.V..L....A.LGFLEK.TFLQS.......KYG.EALLVNFTA..V.LLG.AVV.A.
Retrocopy RRSAVPWHAVLGLLVFALAVGNAQLGFLEKLTFLQSPPARLVGKYGAEALLVNFTAVIVLLLGIAVVIAT

Parental  VAPAAT
          V...AT
Retrocopy VNADAT

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_22 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
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22 ,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34,