RetrogeneDB ID: retro_bdis_11

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:6540803..6542399(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G08360
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G75310
• Aliases: None
• Description: None

Sequence

>retro_bdis_11
ATGGCGGCCATTACCAACTGCTCCATTGCACTCGTAACATCAACCAACGGCCACTCCGCCGCAGCTTCACCCACGACCGC
CGCCCTGCTGCTCCTCTCTCTGATCATCGCCTTCCTGGCATACTTCCACTTGCCATTCTGGGCCGTGCGGAAGGTCCCGG
GCCCTCCGACGCGGTTTCCGCTGGGCCACCTCCACCTCCTGGCCCAGCACGGGCCGGACATCCTCCGCGCCATGGCCCAG
GAGCACGGCCCCATCTTCCGGTTCCACATGGGCCGGCAGCCGCTGGTGATGGCGGCGAGCGCGGAGCTGTGCAAGGAGGT
CGGCATCAAGCGGTTCAGGGACATCCGCAACCGCAGCGCGCCGCCGCCGACGGCCGGCTCGCCGCTGCACCGGGACGCGC
TCTTCCTCGCCAGGGACTCCGCCTGGGCCTCCATGCGGAGCACCGTCGTGCCGCTCTACCAGCCGGCCCGCCTCGCCCAG
CTCGTCCCCACCATGCGGGCCTCCGTCGACGCGCTCGTGGACGCCGTGGACCAGGACCAGGGGAGCTATGTGCCATTCTC
CCAGCTCTCGCTCCGCTTGGCCATCGACATCATCGGGAAGACGGCCTTCGGGATCGAGTTCGGCCTCCTCTCGAAGCAGG
GCACTAATGGCGACGACGAGGCGAGGGAGCTGTTGGGGGAGTACGAGAGGTCCATGGAGTTCATGAAGATGGACCTGTCG
AGCTCGCTGTCCACGATCCTGGGGCTCTTCCTCCCCTGCCTCCAGACCCCCTGCAAGCGGCTGCTGCGGCGCGTGCCGGG
GACGGCGGACCACAAGATGGAGCAGAACGAGCGCCGCCTCTGCCGCCGCATCGACGCCATCATCGCCGCCCGCCGACGCC
GCAGCAGCTCGCCGGCCACGGCGCTGGACTTCATCGCGGCGCTGCTGGAGGACAGCCGGGGACGCGTGGCGGCGCTGGAG
GACCGGCACGTGCGCGCGCTGGCGTACGAGCACCTCATCGCCGGCACCAAGACGACGGCCTTCACGCTCTCCTCCCTCGT
CTACCTCGTCTCCTGCCACCGCCCCGTGGAGGAGAAGCTCCTGGCCGAGCTCGACGCCTTCGGCCCTCAATCTCAATCCC
CTGACGCAGACGAGCTCCACACGAAATTCCCGTACCTGGACCAAATCATCAAGGAATCCATGCGGTTCCACCTGGTGTCG
CCGCTCATCGCCAGGGAGACCTCGGAGGCGGTGGAGATCGGGGGCTACTTGCTCCCGAAGGGCACTTGCGTGTGGCTGGC
GCCGGGGGTGCTGGCCCGCGACGCGGCGCAGTTCCCGGACCCCGACGAGTTCCGGCCCGAGCGGTTCGCGGCGGACGGGG
AAGAGGAGCGCGCGCGGCACCCCTACGCGCACATCCCGTTCGGGATCGGCCCTAGGGCGTGCGTGGGGCACAGGTTCGCG
CTGCAGCAGGTGAAGCTCGCCGTGGTCGGGCTGTACCGCCATTTTGTGTTTCGGCACTCGCCCGACATGGAGTCGCCCGT
GGAGTTCGACTTCGACCTCGTCCTTGGGTTCCGCCATGGCGTCAAGCTCAGGGCCATCAGGAGGACGAACGACTGA

Alignment

ORF - retro_bdis_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.36 %
• Parental protein coverage: 56.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKADLNGSLSMVLGTVAPLLQEPARQLLLRVPGSADRLMDETNRALSGLVDAIVAERAAMEAQSEGEKKN
          .K.DL..SLS..LG...P.LQ.P...LL.RVPG.AD..M....R.L....DAI.A.R......S......
Retrocopy MKMDLSSSLSTILGLFLPCLQTPCKRLLRRVPGTADHKMEQNERRLCRRIDAIIAARRR-RSSSPATALD

Parental  FLSVLLKARESSHAMRELFTADYVSALTYEHLLAGSGSMSFTLSGLAYRVAMHPEVEEKMLSEIDAFGPK
          F...LL...E.S...........V.AL.YEHL.AG.....FTLS.L.Y.V..H..VEEK.L.E.DAFGP.
Retrocopy FIAALL---EDSRGRVAALEDRHVRALAYEHLIAGTKTTAFTLSSLVYLVSCHRPVEEKLLAELDAFGPQ

Parental  DLVPDAEELNTKFTYLEQVLKETMRFYSSSPLVSRETTEDVEIGGYLLPKGTWVWLATGQLSKDPKHFPD
          ...PDA.EL.TKF.YL.Q..KE.MRF...SPL..RET.E.VEIGGYLLPKGT.VWLA.G.L..D...FPD
Retrocopy SQSPDADELHTKFPYLDQIIKESMRFHLVSPLIARETSEAVEIGGYLLPKGTCVWLAPGVLARDAAQFPD

Parental  PYTFRPERFDPEDEECKRRHPYAFLPFGIGPRGCPGQKFAMQQLKLVVIHLYRRYVFRHSPGMEFPLQLE
          P..FRPERF....EE...RHPYA..PFGIGPR.C.G..FA.QQ.KL.V..LYR..VFRHSP.ME.P....
Retrocopy PDEFRPERFAADGEEERARHPYAHIPFGIGPRACVGHRFALQQVKLAVVGLYRHFVFRHSPDMESPVEFD

Parental  FSIVNNFKHGVKLQVIDR
          F..V..F.HGVKL..I.R
Retrocopy FDLVLGFRHGVKLRAIRR

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_11 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G75310	1 retrocopy	retro_bdis_11 ,