RetrogeneDB ID: retro_atau_62

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold60171:8202..8954(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_15320
• Aliases: None
• Description: None

Sequence

>retro_atau_62
GATGAGCAGCTCGCGTTCCTTGAACTGGTCGATCGCATGGACAAGTTGAATTTGGCTGAGATGCACGCGGAGAAAGTCAA
GGCGCTCATGGTTTACGACCCCAAGAGGAAAGACGAAGTCCCGAGCCGCTTCTGCAGCTTCCACCTTGCCAACTTCGACC
TCGATGAGATGTCGAAAGTCCGCTTCTTGGGCCGCCTTATGAAGAATCTGATGCATGTAAGATGGCCGCTTCATCCATCA
ATGTCATCTGCGTGAGGGTTGTCAAAGCCGGTCCCGGTTTCCCGGTCGAGGTTTACGGTAAAATCATTGCGAGGGATGAG
GTCGACTACAAATGCGTCTCTCTGTTCGATCGTGAAAGGGACAATGCCCAGCTGATCAACTCTGAGCAGGATGTGCTAGC
TCTGACAGGTCCGTGCCGAGCATTGGTTACTATGGGCTTGTTGTTTTTTGAGTTTGATTTGAAGATCAAGGGCAAGGGTG
AGCCAGATGAGGATGCACAGTTTAGCAAAGGCGTAATAGCGTACTATCATAACCCGTATAACAAGCGCATCATCGAGCAG
CTACCGAGTTTCGAGAGCACGGTGAAGTTGGTATTGCAACATGTGGCGGCTCCGGTCGCAGCTAGCGTCGAAGTCAATGT
TGTGAAAAAACAGCCTGGTGATGCTGTTGCCCACTTTGATGGGAAAATAACAGTTGGGACTAGCAGAAATTATAGACAGC
ATATGGTTGTTTATGATGGCAATCTGCCTAGC

Alignment

ORF - retro_atau_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.14 %
• Parental protein coverage: 52.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKQPTFLGLLRSTDKSKLDDMHKKKVQELMVYDPKRHSNVFTRFCGFHLANFDLDEKSNAK-LG-PSYDP
          ..Q..FL.L....DK..L..MH..KV..LMVYDPKR...V..RFC.FHLANFDLDE.S....LG.P.Y..
Retrocopy DEQLAFLELVDRMDKLNLAEMHAEKVKALMVYDPKRKDEVPSRFCSFHLANFDLDEMSKVRFLG<PPYEE

Parental  G-VPKMADSSINVISLRIVKTGPDYTYPVEVFGRVIVRDEVDYKCVLLFDREKNNAQLINSEEDMLALTG
          ....KMA.SSINVI..R.VK.GP....PVEV.G..I.RDEVDYKCV.LFDRE..NAQLINSE.D.LALTG
Retrocopy SDACKMAASSINVICVRVVKAGPG--FPVEVYGKIIARDEVDYKCVSLFDRERDNAQLINSEQDVLALTG

Parental  PCRALVTDDLLFFEFDLKIKGKGEHDSEVQFSKGVILYHLDQYHKRFTRQLPSFQSTVKLVLQHVANPVA
          PCRALVT..LLFFEFDLKIKGKGE.D...QFSKGVI.Y....Y.KR...QLPSF.STVKLVLQHVA.PVA
Retrocopy PCRALVTMGLLFFEFDLKIKGKGEPDEDAQFSKGVIAYYHNPYNKRIIEQLPSFESTVKLVLQHVAAPVA

Parental  ASVQVYVLDKQPG---VDFNGKITVGTTGNYRQHMIVYDSSLPS
          ASV.V.V..KQPG.....F.GKITVGT..NYRQHM.VYD..LPS
Retrocopy ASVEVNVVKKQPGDAVAHFDGKITVGTSRNYRQHMVVYDGNLPS

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_62 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_15320	1 retrocopy	retro_atau_62 ,