RetrogeneDB ID: retro_taes_96

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DL_scaff_14470745:2005..3751(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DL_550D9A6C1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_4AL_59D5504B1
• Aliases: None
• Description: None

Sequence

>retro_taes_96
ATGGCGGCGGGTGCGACGACGATGGATGGCACCGTGAATCTCTCCGGCGAGCCGGCGGTGAGGGGCAAGACGGGGGGTTG
GAGGGCGTGCCCCTTCATCCTGGCCAACGAGTGCTGCGAGCGCCTCGCCTACTACGGCATGAGCTCCAATCTGGTCAACT
ACATGATCGACCGCCTCCACCAGGGCAACGCCGCCGCCGCCACCAACGTCAACAACTGGTCCGGCACCTGCTACGTCATG
CCCCTCCTCGGCGCCTTCATCGCCGACGCCTACCTCGGCCGCTTCCGCACCATCGCCGCCTTCATGTCCCTCTACATCGC
CGGCCTCGCCCTCCTCACCCTCACCGCCACCGTGCCCGGCCTCCGCCCGCCCGACTGCGCCGGCTGCAAGCCCGCCGCCG
GCCAGACCGCCGCCTTCTTCACCGCGCTCTACCTCATCGCCGTCGGCACCGGCGGCATCAAGCCCTGCGTCTCCTCCTTC
GGCGCCGACCAGTTCGACGACGCCGACCCGCGCGAGATGCGCAGCAAGAGCTCCTTCTTCAACTGGTTCTACATGTCCAT
CAACGTCGGCGCCCTCGTCGCCTCCTCGGTGCTCGTCTGGGTCCAGATGAACGTCGGCTGGGGCTGGGGATTCGGCATCC
CCGCCGCCGCCATGGCCGTCGCCGTCGTCAGCTTCCTCATGGGGAGCAGGCTCTACAGGTACCAGAAGCCCGGGGGCAGC
CCGCTCACCAGGATGCTGCAGGTCGTGGTCGCCGCCTGCAGGAAGTCGCACGTTCCTCTCCCCGCCGACCCCTCCCTGCT
GCACGAGGTGGCGTCGCCGGACGGCAAGGCCGCCATCGAGGGCAGCAGGAGGCTGGAGCACACGGAGCAGCTGAGGTGCC
TGGACAAGGCCGCCGTGGTGACGACGCCCGGCGGCGCTGAAGAAGAGGACGAGGGCCCGTGGAGGCTGTGCACGGTGACG
CAGGTGGAGGAGCTCAAGAGCATGGTGCGGCTGCTGCCGGTGTGGGCGAGCGGCATCGTCATGTCGGCGGTGTACAGCCA
GATGAGCACCATGTTCGTGCTCCAGGGCAACACCCTCGACCCGCGCATGGGCGCCTCCTTCAAGATCCCCGCCGCCTCGC
TCTCCATCTTCGACACCATCGCCGTCATCGTCTGGGCGCTGGCCTACGACCGGCTCATCGTGCCCGCCGCGCGCCGGATC
ACGGGCCACCCGCGCGGCTTCACGCAGCTCCAGCGCATGGGCATCGGCCTGGTGATATCCATCTTCTCCATGGTGGCCGC
CGGGGTGCTGGAAGTTGTCAGGCTCCACGTCGCCGCCACACACGGCATGCTGGACTCCAAGGAGTACCTGCCCATGTCCA
TCTTCTGGCAGGTGCCGCAGTACTTCATCGTGGGGGCGGCGGAGGTGTTCACGTTCGTGGGGCAGATCGAGTTCTTCTAC
GACCAGTCGCCGGACGCCATGAGGAGCATGGGGTCGGCGCTGTCGCTCACGTCCAACGCGCTGGGCAACTACCTGAGCAC
GCTGCTGGTGGTGATCGTGACGGCCATCTCGACGAGGAACGGCGGCCTCGGGTGGATCCCGGATGACAACCTCAACCGGG
GGCACCTCGACTACTTCTACTGGGTGCTGGCCGTGCTCAGCGCCCTCAACTTCATCGTCTACCTCTGGATAGCAAAGTGG
TACAAGTACAAGGCCACAGCACCTCCTGCAGCAGCTTCAGTCGTTGCCATCGACGACACCAATTAG

Alignment

ORF - retro_taes_96 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.7 %
• Parental protein coverage: 98.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGDGSVDFSGNPVVKEKTGRWKACPFILGNECCERLAYYGISTNLVTYLTKKLHDGNSSAARNVTTWQGT
          T.DG.V..SG.P.V..KTG.W.ACPFIL.NECCERLAYYG.S.NLV.Y....LH.GN..AA.NV..W.GT
Retrocopy TMDGTVNLSGEPAVRGKTGGWRACPFILANECCERLAYYGMSSNLVNYMIDRLHQGNAAAATNVNNWSGT

Parental  CYLTPLIGAILADAYWGRYWTIATFSTIYFIGMSVLTLSASVPMLMPPSCEGAICPEASPLQYTVFFLGL
          CY..PL.GA..ADAY.GR..TIA.F...Y..G...LTL.A.VP.L.PP.C.G..C..A...Q...FF..L
Retrocopy CYVMPLLGAFIADAYLGRFRTIAAFMSLYIAGLALLTLTATVPGLRPPDCAG--CKPAAG-QTAAFFTAL

Parental  YLIALGTGGIKPCVSSFGADQFDDTDPAERIQKGSFFNWFYFSINIGALISSSFLVWVQDNLGWGLGFGI
          YLIA.GTGGIKPCVSSFGADQFDD.DP.E...K.SFFNWFY.SIN.GAL..SS.LVWVQ.N.GWG.GFGI
Retrocopy YLIAVGTGGIKPCVSSFGADQFDDADPREMRSKSSFFNWFYMSINVGALVASSVLVWVQMNVGWGWGFGI

Parental  PTVFMGLAIISFFAGTSLYRFQKPGGSPITRVCQVVAATLRKWNAPVPEDSSLLYELA--DGVSAIEGSR
          P...M..A..SF..G..LYR.QKPGGSP.TR..QVV.A..RK...P.P.D.SLL.E.A..DG..AIEGSR
Retrocopy PAAAMAVAVVSFLMGSRLYRYQKPGGSPLTRMLQVVVAACRKSHVPLPADPSLLHEVASPDGKAAIEGSR

Parental  QLEHTDELRCLDKAATITDLDVKEDSFNNPWRVCTVTQVEELKILVRMFPVWATTIVFSAVYAQMSTMFV
          .LEHT..LRCLDKAA..T.....E.....PWR.CTVTQVEELK..VR..PVWA..IV.SAVY.QMSTMFV
Retrocopy RLEHTEQLRCLDKAAVVTTPGGAEEEDEGPWRLCTVTQVEELKSMVRLLPVWASGIVMSAVYSQMSTMFV

Parental  EQGMVLDPTIG-SFKIPPASLSTFDVVSVIIWVPIYDSILVPIARRFTGKERGFSELQRMGIGLVISILA
          .QG..LDP..G.SFKIP.ASLS.FD...VI.W...YD...VP.ARR.TG..RGF..LQRMGIGLVISI..
Retrocopy LQGNTLDPRMGASFKIPAASLSIFDTIAVIVWALAYDRLIVPAARRITGHPRGFTQLQRMGIGLVISIFS

Parental  MSAAAVLEIKRLAIAREAHLVDQNVPVPLSILWQIPQYFLVGASEVFTFIGALEFFYDQSPDAMRSLCSA
          M.AA.VLE..RL..A......D.....P.SI.WQ.PQYF.VGA.EVFTF.G..EFFYDQSPDAMRS..SA
Retrocopy MVAAGVLEVVRLHVAATHGMLDSKEYLPMSIFWQVPQYFIVGAAEVFTFVGQIEFFYDQSPDAMRSMGSA

Parental  LQLITTALGNYLSAFILTMVAYFTTRGGRPGWIP-DNLNEGRLDYFFWLLAGLSFLNFLVYVLCANRFKS
          L.L...ALGNYLS......V....TR.G..GWIP.DNLN.G.LDYF.W.LA.LS.LNF.VY...A...K.
Retrocopy LSLTSNALGNYLSTLLVVIVTAISTRNGGLGWIPDDNLNRGHLDYFYWVLAVLSALNFIVYLWIAKWYKY

Parental  KKAA
          K..A
Retrocopy KATA

Legend:

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

Expression

RNA-Seq

Triticum aestivum was not studied using RNA-Seq expression data.

ChIP-Seq

Triticum aestivum was not studied using ChIP-Seq data.

EST

Triticum aestivum was not studied using EST data.

TSS

Triticum aestivum was not studied using FANTOM5 data.

Lab

retro_taes_96 was not experimentally validated.

Homology

Retrocopy orthology:

Triticum aestivum 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
Oryza sativa indica	BGIOSGA009904	1 retrocopy	retro_oind_36,
Hordeum vulgare	MLOC_58062	1 retrocopy	retro_hvul_66,
Oryza glumaepatula	OGLUM02G34910	1 retrocopy	retro_oglu_17,
Oryza glaberrima	ORGLA03G0409900	1 retrocopy	retro_ogla_29,
Oryza rufipogon	ORUFI03G33580	1 retrocopy	retro_oruf_5,
Oryza sativa japonica	OS03G0719900	1 retrocopy	retro_osat_25,
Triticum aestivum	Traes_4AL_59D5504B1	1 retrocopy	retro_taes_96 ,