RetrogeneDB ID: retro_sita_23

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 9:304443..305538(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si036296m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si024870m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_23
ATGGATGATACATCAGCCAAGCCGCGCAACCTGGGCGGGTCGCTGCCCGTCCCCAACGTGCAGGACCTCGCCGCGCGCCC
CGCCGACGAGCTCACGCCGGCCGTCCTCCACCGCTACCTCCGCGGCGCCGACGCTCCAGCGCTCTCTGCTGCCACCGTCA
CGGTGCCCGTCGTGGACCTCGGCAGGCTGCTCGACCCGTCGTCGTCCATGGATATTGAGGCCGCCAGCCTGAGGGCCGCC
TGCGAGGACTGGGGCTTCTTCCAGGTCGTCAACCACGGCGTGCCCGACGAGGTCATCCACGACGTCAGGGAGGACCTCAA
GGCCTTCTTCCAGCTCCCGCTCGCGGAGAAGCAGGCCCTTGCGCAGGGGCCCGGCGGGATCGAGGGCTACGGGCAGGCCT
TCGTCGTCTCCGAGGACCAGAAGCTGGACTGGGCCGACATGCTCTTCCTCTCCACGCTGCCGCCCGAGTACCGCTCCCTC
AACTTCTGGCCTTCCCGCCCCGCCACTTTCGGCGGCTCGCTCCAGCGCTACGCCGCGGAGGTGCAGCGGGTGGCCGCCGG
CCTGCTCCGAGCCATGGCCAGGAACCTGGGCGTGGCGGACACGGAGGAGATGACGAGGATCGCCGCCGCGCAGGGCATGC
GGATCAACTACTACCCGCCGTGCCCGCAGGCGCACGACAAGGTGCTGGGCCTGTCGCCGCACTCCGACGCCGTCGGGCTC
ACGCTGCTGCTGCAGGCGAGCCCCGTGGCCGGCCTGCAGATCAGGCGGGAGGGCGCCTGGATCCCGGTGGAGCCGCTGCC
GGGGGCCCTGATCGCCAACGTCGGCGACGTCATCGAGGTGCTCACCAACGGCAGGTACAAGAGCATCGAGCACAGGGCGG
TGGTCAACGCGCGCCACGAGCGGATCTCCGTCGCCGCCTTCCACACCGCCATGTTCGGCGGCACGTACGGGCCGCTGGAG
GAGATCATCGTCGGACAAGGCGAGGCGCCGCGCTACAGGACCGTCGGCGTCGAGGACTACGTAAAGCTCGTGCTGTCCAG
CAAGCTCGAGGGAAAGAACATCATGGACGCCATGAAGATCAACAATGCTCCTTGA

Alignment

ORF - retro_sita_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.28 %
• Parental protein coverage: 95.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIPVRNVQALAASSADELTAETLDRYIRPGIDQDAVLEEHSDELPVVDLGRLLNPES-WEEEAAKLRFAC
          ..PV.NVQ.LAA..ADELT...L.RY.R.G.D..A.L.......PVVDLGRLL.P.S....EAA.LR.AC
Retrocopy SLPVPNVQDLAARPADELTPAVLHRYLR-GADAPA-LSAATVTVPVVDLGRLLDPSSSMDIEAASLRAAC

Parental  EEWGFFQVLNHGVPEEVIVNIKRDIQEFFNLPLEVKNAYAQRPGDLQGYGQAYVFSEDQKLDWADMLGIL
          E.WGFFQV.NHGVP.EVI.....D...FF.LPL..K.A.AQ.PG...GYGQA.V.SEDQKLDWADML...
Retrocopy EDWGFFQVVNHGVPDEVIHDVREDLKAFFQLPLAEKQALAQGPGGIEGYGQAFVVSEDQKLDWADMLFLS

Parental  TQPPEARDTKLWPAQPLTFRKSVEDYSAELKKIAHSIASIIAKMLNI-KPELMDDKYAVQVLRMNYYPPC
          T.PPE.R....WP..P.TF..S...Y.AE....A.......A..L.....E.M....A.Q..R.NYYPPC
Retrocopy TLPPEYRSLNFWPSRPATFGGSLQRYAAEVQRVAAGLLRAMARNLGVADTEEMTRIAAAQGMRINYYPPC

Parental  MSMPEKVLGFSPHSDGSFFTILKEVNSVNGLQIRRHGAWIPVKPHPKAFLVNVGDLLEIMTNGKYKSIEH
          .....KVLG.SPHSD....T.L.....V.GLQIRR.GAWIPV.P.P.A...NVGD..E..TNG.YKSIEH
Retrocopy PQAHDKVLGLSPHSDAVGLTLLLQASPVAGLQIRREGAWIPVEPLPGALIANVGDVIEVLTNGRYKSIEH

Parental  RVTIDAHMERLSVSAFINPKFDDVVSP---VLGSTTEEVLYKTVSVEDYMKHYMSNKLDGKKALDHAKVS
          R....A..ER.SV.AF....F.....P.........E...Y.TV.VEDY.K...S.KL.GK...D..K..
Retrocopy RAVVNARHERISVAAFHTAMFGGTYGPLEEIIVGQGEAPRYRTVGVEDYVKLVLSSKLEGKNIMDAMKIN

Parental  N
          N
Retrocopy N

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_23 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.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Setaria italica	Si024870m.g	1 retrocopy	retro_sita_23 ,