RetrogeneDB ID: retro_bdis_34

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:41436988..41438230(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G41160
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G20760
• Aliases: None
• Description: None

Sequence

>retro_bdis_34
ATGTCGGTTTTAATTGTCACCAGCGTGGGCGACATCACGGTGGATCTCCACACCTTTTGCTGCCCCCTCACCACCAGGAA
CTTTCTCAAGCTCTGCAAGATGAAGTATTACAAGGGGTGTTTGTTTCACAAAGTGGAGAAGGATTTCTTGGCACAATCCG
GGGACCCAACTGGAACAGGCAGCGGAGGTGATTCTGTGTACAAGTTCCTTTATGGTGATCAAGCTCGATTTTTCAGTGAT
GAGATCCGCCCAAAATTGAGGCATTCACGAATTGGCACGGTTGCTATGGCAAGTGCAGGTGAAAACTGCAATGCCTCGCA
GTTCTACATCACCTTGCGCGCCGATATTGACTACCTTGATGATAAACACACCGTGTTTGGGATCGTTGCTGAAGGTCTTG
ACACACTGAAGAAGATGAATGAAGCATATGTTGATGACAGGAAAAGACCATTCAAGGACATTAGGATTAAGCATACATAT
ATCTTGGACGATCCATTCAGTGATCCTCCTCAGCTTGCTAAATTTATTCTTGAAAGTTCTCCCATTGGGAAGCCACGTGA
TGAGGTTGCAGAAGAGCGGTTAGACGACGGTTGGATGCCTTCCGATGAAACAACGACTCCTAAACAGCTGGAGGAGATGA
TCCGCTCCAAAGAAGCACATGCTAACGCAGTGATCCTTGAAAGTGTTGGAGACATTCCAGACGCTGACGTCAAACCACCG
GACAATGTCTTATTTGTAGCCAAACTCAATCCGATAACACGAGATGAAGATTTGTATACAATCTTTTCTCGATTTGGAAC
TGTGGAATCAGCTGAAATAATTCGTGATTACAAGACTGGAGATAGCTTGTGCTATGCCTTCATTGAATTTGAGACAAAAG
AAGCTTGTGAACGTTCACGTGTCGATATGGACAACTGTCTCATTGACGACCGGAGGATCCATGTTGATTTCAGTCAAAGC
GTTTCAAAATTGTGGTGTCAGTTCAGAAATAGCGAACCAGGTGCAAAAAAAGATGGTTGGTTCAGGCGTGGTCGAGATAG
AGATCAAGGTGTTGAGCGAAAAACCAAAGGCCATGTTCTAAAAGATGAGAACACTCAACGAGATGGCTGCAATAACCGTC
GAAGTTACGATATGGTCTTTCAGGAGCCCGGTGCCCATCAGCAAGATCGATATGCTAGTCGAAGAAAAATTCAAAAAGTG
AATGGTCAGGATAGATACAATGATCATGGCAACAGAAAATAA

Alignment

ORF - retro_bdis_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.01 %
• Parental protein coverage: 63.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVLIVTSVGDIELDLHTDLCPLTTKNFLKLCKMKYYNGCLFHKVEKDFLAQSGDPTGTGSGGDSVYKFL
          MSVLIVTSVGDI..DLHT..CPLTT.NFLKLCKMKYY.GCLFHKVEKDFLAQSGDPTGTGSGGDSVYKFL
Retrocopy MSVLIVTSVGDITVDLHTFCCPLTTRNFLKLCKMKYYKGCLFHKVEKDFLAQSGDPTGTGSGGDSVYKFL

Parental  YGDQARFFNDEIRPELRHSKTGTVAMASAGENCNASQFYITLRDEVDYLDDKHTVFGTVAEGFDTLTKIN
          YGDQARFF.DEIRP.LRHS..GTVAMASAGENCNASQFYITLR...DYLDDKHTVFG.VAEG.DTL.K.N
Retrocopy YGDQARFFSDEIRPKLRHSRIGTVAMASAGENCNASQFYITLRADIDYLDDKHTVFGIVAEGLDTLKKMN

Parental  EAYVDDKGRPFKNIRIKHTYILDDPFDDPPQLAELIPDNSPLGKPHDEVAEERLEDSWVPLDETVDPEQL
          EAYVDD..RPFK.IRIKHTYILDDPF.DPPQLA..I...SP.GKP.DEVAEERL.D.W.P.DET..P.QL
Retrocopy EAYVDDRKRPFKDIRIKHTYILDDPFSDPPQLAKFILESSPIGKPRDEVAEERLDDGWMPSDETTTPKQL

Parental  EEMIRSKEAHANAVILESVGDIPDAEVKPPDNVLFVCKLNPVTQDEDLYTIFSRFGTVTSAEIIRDFKTG
          EEMIRSKEAHANAVILESVGDIPDA.VKPPDNVLFV.KLNP.T.DEDLYTIFSRFGTV.SAEIIRD.KTG
Retrocopy EEMIRSKEAHANAVILESVGDIPDADVKPPDNVLFVAKLNPITRDEDLYTIFSRFGTVESAEIIRDYKTG

Parental  DSLCYAFIEFEVKEACERAYFKMDNCLIDDRRIHVDFSQSVSKLWGQFRQSKRNANKDGCFKCG
          DSLCYAFIEFE.KEACER....MDNCLIDDRRIHVDFSQSVSKLW.QFR.S...A.KDG.F..G
Retrocopy DSLCYAFIEFETKEACERSRVDMDNCLIDDRRIHVDFSQSVSKLWCQFRNSEPGAKKDGWFRRG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brachypodium distachyon was not studied using RNA-Seq expression data.

ChIP-Seq

Brachypodium distachyon was not studied using ChIP-Seq data.

EST

Brachypodium distachyon was not studied using EST data.

TSS

Brachypodium distachyon was not studied using FANTOM5 data.

Lab

retro_bdis_34 was not experimentally validated.

Homology

Retrocopy orthology:

Brachypodium distachyon 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G20760	1 retrocopy	retro_bdis_34 ,
Aegilops tauschii	F775_03869	1 retrocopy	retro_atau_2,
Hordeum vulgare	MLOC_58863	1 retrocopy	retro_hvul_70,