RetrogeneDB ID: retro_sita_22

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:5739416..5740439(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si024272m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si024398m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_22
ATGGAGAACATGCTCCACCTGACCCCGTCCCACGCGTCGTCGATCCCGGACTCCTTCGTCCTGCCGGCCGACCACCTCCG
GCCGGCGACGACCGCCGACGTTTCTGTCTCCCTGCCAGTCATCGACATGTCCCGCGGCCGCGACGAGGTCCGCCGTGCCA
TCCTCGACGCCGCCAAGGAGCACGGCTTCTTCCAGGTGGTGAACCACGGCGTCCCCGAGCAGGTGCTGCGCGACATGGAG
GCGGTGTGCCACGACTTTTTCAAGATGCCCGCGGAGGAAAAGGCGGAGTTCTACTCGGAGGACAAATCCAAGCCTAACAG
GCTCTTCTCCGGCTCCGTCTACGAGACCCTCGGCGAGAGGTACTGGCGCGACTGCCTCTGCCTCGTCTACCCCTTGCCCG
CCGGCGACACCTCGGACTGGCCCCACAAGCCACAGAGGCTCAGAGAGTTCGTTGAGAATTACACCGTGCTGACAAGAGGC
CTGGCCATGGAGACCCTTCGCCTGCTGTGCGAGGGCATGGGCCTCCGGCCAGACTACTTCGTCGGCGACATCAGCGGCGG
CGTGGCCGTCGACATCAACCACTACCCGCCGTGCCCGGAGCCGGGCAGGACGCTGGGCCTGCCGCCACACTGCGACCGGG
AGCTCATCACGGTCCTCCTCCCCGGCGCCGTCCCAGGCCTCGAGGTCGCCTACAAGGGCGACTGGATCAAGGTCCAGCCA
GTCCCCAACTCCTTCGTCGTCAACTTCGGCCTGCAGCTCGAGGTCGTGACCAACGGGACGCTCAAGAGCGTGGAGCACCG
CGTGGTCACCAACTCGGCGGCGCCGCGGATGTCGGTGGCCACGTTCGTCGCGCCGGCGGACGACTGCGTCGTCGGCCCCG
CCGAGGAGTTCGTCGGCGAGGGCAACCCGCCGCGCTACCGCACCGTCAGGTTCAGGGACTTCAAGCGCATGTATAACGTT
GTGAATCTGGGGTCCTCGCTCAACCAGATTACTAGCGTCAAGAACAACCGGAAGGAGATGTGA

Alignment

ORF - retro_sita_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.43 %
• Parental protein coverage: 98.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNMLQLLPTHTSAIPDCFVLPADQLKAATIA--AVLLPVIDMSRGRDEVRRAILDAGREHGFFQVINHGV
          .NML.L.P.H.S.IPD.FVLPAD.L..AT.A...V.LPVIDMSRGRDEVRRAILDA..EHGFFQV.NHGV
Retrocopy ENMLHLTPSHASSIPDSFVLPADHLRPATTADVSVSLPVIDMSRGRDEVRRAILDAAKEHGFFQVVNHGV

Parental  PEQVLRDMEAVCHEFFQLPAADKAEFYSEDKSKPNRLFSGTNYETLGERYWRDCLRLVYPLPSGDTSGWP
          PEQVLRDMEAVCH.FF..PA..KAEFYSEDKSKPNRLFSG..YETLGERYWRDCL.LVYPLP.GDTS.WP
Retrocopy PEQVLRDMEAVCHDFFKMPAEEKAEFYSEDKSKPNRLFSGSVYETLGERYWRDCLCLVYPLPAGDTSDWP

Parental  HKPLRLREVVGNYTGLARGLAMEILQLLCEGLGLRPDYFVGDISGGRVALDINSYPPCPDPSRTLGLPPH
          HKP.RLRE.V.NYT.L.RGLAME.L.LLCEG.GLRPDYFVGDISGG.VA.DIN.YPPCP.P.RTLGLPPH
Retrocopy HKPQRLREFVENYTVLTRGLAMETLRLLCEGMGLRPDYFVGDISGG-VAVDINHYPPCPEPGRTLGLPPH

Parental  CDRDLITVLLPGAVPGLEVAYEGDWIKVQPVPNSFVVNFGLQLEVVTNGMLKSVEHRAATNSAEPRMSVA
          CDR.LITVLLPGAVPGLEVAY.GDWIKVQPVPNSFVVNFGLQLEVVTNG.LKSVEHR..TNSA.PRMSVA
Retrocopy CDRELITVLLPGAVPGLEVAYKGDWIKVQPVPNSFVVNFGLQLEVVTNGTLKSVEHRVVTNSAAPRMSVA

Parental  TFIVPADDCVVGPAEEFVGEDNPPRYRTMRVRDFKRMHNVVNLGSSLNQITNLKNNQK
          TF..PADDCVVGPAEEFVGE.NPPRYRT.R.RDFKRM.NVVNLGSSLNQIT..KNN.K
Retrocopy TFVAPADDCVVGPAEEFVGEGNPPRYRTVRFRDFKRMYNVVNLGSSLNQITSVKNNRK

Legend:

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

Expression

RNA-Seq

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq

Setaria italica was not studied using ChIP-Seq data.

EST

Setaria italica was not studied using EST data.

TSS

Setaria italica was not studied using FANTOM5 data.

Lab

retro_sita_22 was not experimentally validated.

Homology

Retrocopy orthology:

Setaria italica 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si024398m.g	1 retrocopy	retro_sita_22 ,