RetrogeneDB ID: retro_sita_57

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 9:32232378..32233074(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si032257m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_57
CAGCTTGAGGATGAGCACACATTTGGTTCTTACAAGATTGAGAAGGAGTCCATGCTACGCCTTACACTGCGCCTTCGTTG
TGGACCTTGTCCAAGAAATATTCAAGTGAAGATGATCACTGGCAAAACCATCACTCTCCAGGCGGAGCCATCGGACACCA
TTAACAACCTCTTGGCAAAGATTCGTAGCCACCAGAGGCTCCTTTTTGATGGCAAGCAGCTTGAGGAAAAACTTACAATT
GCACATTACGGCGTCCCAGTAGAGTCTACCATTTATGATGATTTCGATATGCAGATCTTCGTGAAGATGCCCAGTGGTAA
GACCATCATCCTCGAGGTGGAGCCATCAGACACCATCAGCAGTGTCAAGGCAAAGATACGGGACCAGCAGAAGATCATCT
TTAACGGCAGGAAGCTCAACGATAACAGCAAACTTGTGGATTACGACATTCAGAAAGAGTCCACCCTGCACCTTGACCTT
TGTCAGAATGGTGCCATGCAGATTTTCGTGAAGGCGCTCCCTAGCAAGGACATCAGCCTTAAGAAGGTTCGCACAATGGA
AACAATGGGCAATGTGATGGCGAAGATTCAGGCCCAGCAGAGGCTTATCTATGAAGGCAAGCTGCTTGAGCATAGGAGGA
CGCTTGCCGACTACAACATCCAGACAGAATCAACCCTGTTCCTTGACTGTGGCATG

Alignment

ORF - retro_sita_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.16 %
• Parental protein coverage: 90.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLESSDLIVNIKAKIQEIFRRVLR-RPANWIGDIYVKMLAGSDITLDVEPSDKIDNVREKIHGYQRLVFA
          .LE........K.......R..LR.R.......I.VKM..G..ITL..EPSD.I.N...KI...QRL.F.
Retrocopy QLEDEHTFGSYKIEKESMLRLTLRLRCGPCPRNIQVKMITGKTITLQAEPSDTINNLLAKIRSHQRLLFD

Parental  GKYLEDGGTLADYDIQNESTLHLDFGMQILVKTSTGKTITMQVEPSDTIRRVKAKIQDQQRLLFDGKHLN
          GK.LE...T.A.Y....EST...DF.MQI.VK...GKTI...VEPSDTI..VKAKI.DQQ...F.G..LN
Retrocopy GKQLEEKLTIAHYGVPVESTIYDDFDMQIFVKMPSGKTIILEVEPSDTISSVKAKIRDQQKIIFNGRKLN

Parental  GWGKLADYNVKKESTLQLDLCPQGGMQVFVKALPRKTIRLKLVRS-DTIGRLKAMIQDQQRLLFDGKQLE
          ...KL.DY...KESTL.LDLC..G.MQ.FVKALP.K.I.LK.VR...T.G...A.IQ.QQRL...GK.LE
Retrocopy DNSKLVDYDIQKESTLHLDLCQNGAMQIFVKALPSKDISLKKVRTMETMGNVMAKIQAQQRLIYEGKLLE

Parental  DGRRLADYNIQKGSTQHLDLGL
          ..R.LADYNIQ..ST..LD.G.
Retrocopy HRRTLADYNIQTESTLFLDCGM

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_57 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	Si032257m.g	1 retrocopy	retro_sita_57 ,