RetrogeneDB ID: retro_bdis_16

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:803023..804595(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G01190
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G61140
• Aliases: None
• Description: None

Sequence

>retro_bdis_16
ATGGCGGGCAAGATCAAGACGGTGGTGGTGTTGGTGCAGGAGAACCGGTCGTTCGACCACATGCTGGGCTGGATGAAGTC
CCTCAACCCGGAGATCGACGGCGTCACGGGAACCGAGACCAACCACGTCATCGCCGGCGACGCGTCCTCCAAGGCCGTCG
TCTTCTCCGACAAGTCCGAGTACGTGGACCCGGACCCGGGCCACTCCATCCAAGCCATCTACGAGCAAGTCTACGGCACG
CCCTTCGTCGACGCCACCGCCACACCGATCACCCCTTCTTCCCCGGCGACGATGGCCGGCTTCGCGCAGCAAGCCGAGAA
GGAGAAGCCCGGGATGTCGGAGACCGTGATGAGCGGGTTCAAGCCCGACGCCGTGCCCGTTTACAAGGAGCTCGCCAAGG
AGTTCGCCGTGTGCGACCGCTGGTTCGCGTCGAACCCGGCGTCGACGCAGCCCAACCGGCTCTTCGTGCACTCCGGCACC
TCCCATGGCCTCGTCAGCAACGACACTAAAACCCTCGTCGCCGGCTTGCCACAGAAGACCATCTTTGACAGTCTCGACGA
TGCCGGCCTTTCGTTCGGCATCTACTACCAGTTCCCGCCGGCCACGCTCTTGTACCGCAACCTCCGGCAGCTCAAGTATC
TTGACAACTTCCATCAGTACGATCTCTCGTTCCGTCGCCATTGCCGGGAAGGGAAGCTTCCCAATTATGTCGTCGTCGAG
CAGCGGTACTTCGATCTCGCAAATATAGGGCTCCCCGGGAACGATGATCACCCTTCCCATGATGTCGGCGAGGGGCAGAG
GTTCGTGAAGGAGGTGTATGAAGCTCTCAGGGCCGGGAAGCAATGGGAGGAGACGCTGCTAGTTGTGACGTATGACGAGC
ATGGGGGATTTTACGACCATGTCCCGCCGCCTTCCGGCGCCGGCGTCGTGCCCAGCCCCGACGGCATCGTCTCTGCGCCG
CCGTTCTTCTTCAACTTCGACCGCCTCGGGGTCCGCGTCCCGGCCTTCTTCATTTCGCCGTGGATCGAGCCTGGGACGGT
GGTGCACCGGCCGGCCCATGGGCCGGAGCCCACGTCGGAGTTCGAGCACTCCTCCATCCCAGCCACCGTGAAGGCCATCT
TCGGCCTCCCGAGCTTCCTCACCAAGCGCGACGCCTGGGCCGGGACATTTGACACCGTGCTCACCCGGCAAACGCCGCGG
AAGGACTGCCCTACCAAGCTGCCGGAGCCGGTGAAGATGAAGCGTCTGACGGCGGTGGCGGCGGCGGCGCCGGTGATCTC
GGAGTTCCAGGCGGAGCTGGTGCAGCTGGCGGCGGCGCTCAACGGCGACCACGCCAGGGAGGACTACCCGGAGAAGCTGG
TGGAGGGCATGACGGTGCCGGAGGCGGTCAGCTACTGCAACGACGCCTTCAAGGCGTTCCGCGACGAGTGCGAACGCTGC
AAGAGCTGCGGCATGGATGGGTCCCATGTCCCCATCTTGCCTCTGCCGGCGCCGCCAGCACCACCGGCGCCGGAGAAGAA
GAATAGCTTCCCGTCCAAGATTCTGGCTTGCTTTGCGTGTGGCCGTTCTTAG

Alignment

ORF - retro_bdis_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.08 %
• Parental protein coverage: 72.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGPAKMNGFVQQATSIGGGNMTDAVMHGYKPDAVAVYKELVSQFAVCDRWFASVPSSTQPNRLFVHSGTS
          S.PA.M.GF.QQA.....G.M...VM.G.KPDAV.VYKEL...FAVCDRWFAS.P.STQPNRLFVHSGTS
Retrocopy SSPATMAGFAQQAEKEKPG-MSETVMSGFKPDAVPVYKELAKEFAVCDRWFASNPASTQPNRLFVHSGTS

Parental  GGATSNNPELLAEGYPQRTIFDNIYDAGLSFGVYFQDVPAVLFYRNLRKIKYLLKFHPFHNTFRDHAQSG
          .G..SN....L..G.PQ.TIFD...DAGLSFG.Y.Q..PA.L.YRNLR..KYL..FH.....FR.H...G
Retrocopy HGLVSNDTKTLVAGLPQKTIFDSLDDAGLSFGIYYQFPPATLLYRNLRQLKYLDNFHQYDLSFRRHCREG

Parental  NLPNYAVVEQHYMD--SKSHPANDDHPSHDVYQGQMFIKEIYETLRASPQWNETLMVITYDEHGGFFDHV
          .LPNY.VVEQ.Y.D......P.NDDHPSHDV..GQ.F.KE.YE.LRA..QW.ETL.V.TYDEHGGF.DHV
Retrocopy KLPNYVVVEQRYFDLANIGLPGNDDHPSHDVGEGQRFVKEVYEALRAGKQWEETLLVVTYDEHGGFYDHV

Parental  PTP--VDNVPSPDGIVGPPPYNFEFNRLGVRVPTIFISPWIEKGTVVHGPNGSPTPNSQYEHSSIPATVK
          P.P.....VPSPDGIV..PP..F.F.RLGVRVP..FISPWIE.GTVVH.P...P.P.S..EHSSIPATVK
Retrocopy PPPSGAGVVPSPDGIVSAPPFFFNFDRLGVRVPAFFISPWIEPGTVVHRPAHGPEPTSEFEHSSIPATVK

Parental  KLFNLPQDFLTRRDAWAGTFESVVKTRTEPRTDCPETLPMPTRIRQTDANEEAK--LSSFQQEIVQLAAV
          ..F.LP..FLT.RDAWAGTF..V..TR..PR.DCP..LP.P.......A...A....S.FQ.E.VQLAA.
Retrocopy AIFGLP-SFLTKRDAWAGTFDTVL-TRQTPRKDCPTKLPEPVKMKRLTAVAAAAPVISEFQAELVQLAAA

Parental  LNGDHQLTSLQERIRDRMNVREGTAYMRRAVRRFFEAGLSAKRMGV
          LNGDH......E.....M.V.E...Y...A...F.......K..G.
Retrocopy LNGDHAREDYPEKLVEGMTVPEAVSYCNDAFKAFRDECERCKSCGM

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_16 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA000088	1 retrocopy	retro_oind_49,
Brachypodium distachyon	BRADI2G61140	1 retrocopy	retro_bdis_16 ,
Leersia perrieri	LPERR01G38640	1 retrocopy	retro_lper_20,
Oryza barthii	OBART01G44250	2 retrocopies	retro_obar_19, retro_obar_5,
Oryza glumaepatula	OGLUM01G48550	1 retrocopy	retro_oglu_24,
Oryza nivara	ONIVA01G50380	1 retrocopy	retro_oniv_1,
Oryza glaberrima	ORGLA01G0381200	1 retrocopy	retro_ogla_34,
Oryza rufipogon	ORUFI01G47680	2 retrocopies	retro_oruf_3, retro_oruf_32,