RetrogeneDB ID: retro_atau_5

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold38818:10793..11747(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_15790
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_29675
• Aliases: None
• Description: None

Sequence

>retro_atau_5
ATGTACGCCAGCACCTGCTCCGCGGCCGACGAGCGCATGTACTGCCCGGAGTGCCGCCGCGCGACGGAGGTTGTCCTGGA
CCACGGCACCGGCGACACCATCTGCACCGAGTGCGCGCTCGTCCTCGACGCGCACTACATCGACGAGGGGTCCGCGTGGC
GCAACTTCGCCGACGACGGCGGCGGCGAGGACCGCGACCCCAACCGCGTCGGCGCCTCCGGCGACCCCTTCCTCGCCGCC
AAGCTCTCCACCGTCATCGACTACACCAACAAGCCCAAGAAGTCCTCCGCCACCGGCGTGGCGACAAAGGCCCCGCCCAG
GATGTCGGTGCCGGACGCGGGGGCGGCCTCCGAAAACACCCTCGTCGACGGCTTCCGCGGCATCTCCGACATGGCCGACC
GGCTCGGCCTCGTGGCCACCATCCGGGACCTGGCCAAGGAGACGTTCAAGAAGCTGGACGAGGCCAAGGGCTGCCCGCGC
GGCCGGAAGCGGGACTCCGTCTACGCCGCCTGCCTCTACATCGCCTGCCGCAACCTCGGCATGCCGCGCACGTACAAGGA
GCTCGCCTCCGTCACCGCCGGGGGCGTGGCTGCCAAGAAGGACGTCGGCAAGATGACGACGCACATCAAGAAGCTCCTCG
GGGAGGAGGACGGCCAGGTGATGGACATCGGCGTCGTCAGCGCATCCGACTACCTGCGCCGCTTCTGCTCCCGGCTCGGC
CTGGGCAACCAGGAGGTGCGCGACGCGCAGGAGGCCGTGCGGAGGGTCGAGGAAGGGCTCGACGTGCGCCGCAACCCGGA
GTCCGTCGCCGCCGCCATCATCTACATGGTCGTGCAGCGTGCCGGCGCCAGCAGGTCCGCCAAGGACGTGTCCGTCGCCA
CCGGCGTGGCCGAGGGCACCATCAAGGAGGTGCACAAGGACCTCGCCCCACACGCACAGATGCTCTTCGGCTGA

Alignment

ORF - retro_atau_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.59 %
• Parental protein coverage: 91.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADRLGLVATIKDRANEIYKKVEDLKSI-RGRNQDAILAACLYIACRQEDRPRTVKEICSVANG--ATKK
          MADRLGLVATI.D.A.E..KK....K...RGR..D...AACLYIACR....PRT.KE..SV..G..A.KK
Retrocopy MADRLGLVATIRDLAKETFKKLDEAKGCPRGRKRDSVYAACLYIACRNLGMPRTYKELASVTAGGVAAKK

Parental  EIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRFCSTLGMNNTAVKAAQEAVQRSEE-LDIRRSPISIA
          ..G.....I.K.L..E.GQ.M..G...A.D.LRRFCS.LG..N..V..AQEAV.R.EE.LD.RR.P.S.A
Retrocopy DVGKMTTHIKKLLGEEDGQVMDIGVVSASDYLRRFCSRLGLGNQEVRDAQEAVRRVEEGLDVRRNPESVA

Parental  AAVIYMITQLSEDKKPLKDISLATGVAEGTIRNSYKDLYPYAARL
          AA.IYM..Q........KD.S.ATGVAEGTI....KDL.P.A..L
Retrocopy AAIIYMVVQRAGASRSAKDVSVATGVAEGTIKEVHKDLAPHAQML

Legend:

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

Expression

RNA-Seq

Aegilops tauschii was not studied using RNA-Seq expression data.

ChIP-Seq

Aegilops tauschii was not studied using ChIP-Seq data.

EST

Aegilops tauschii was not studied using EST data.

TSS

Aegilops tauschii was not studied using FANTOM5 data.

Lab

retro_atau_5 was not experimentally validated.

Homology

Retrocopy orthology:

Aegilops tauschii 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G36290	1 retrocopy	retro_bdis_39,
Aegilops tauschii	F775_29675	1 retrocopy	retro_atau_5 ,
Hordeum vulgare	MLOC_10647	1 retrocopy	retro_hvul_45,
Medicago truncatula	MTR_7g091230	2 retrocopies	retro_mtru_26, retro_mtru_3,
Sorghum bicolor	Sb02g031020	1 retrocopy	retro_sbic_35,