RetrogeneDB ID: retro_sbic_44

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:21531600..21532887(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g012560
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb07g006050
• Aliases: None
• Description: None

Sequence

>retro_sbic_44
ATGAGGAGGCTTTTACGTCGTACAACAAGAAGCACAGGCAGAGCTGGTGCTAAGGCGCCGTTGATGTTATGGTGGGCAGC
ACCGGCCATCTGCTCTGCGCTTCTCGCCGTCCTGCTCGCCTCCAGATCATCGTTCTACCTCCGGCAGCCTGCTTCTCCTC
CCTACACCTCCCCCGGGGCGGAAGCGGAAGCAGAAGCGGAAGCGGAAGAGGGCCGGCACCACCACCACCGGCGCCGGGCG
TGCGACGACCAGGCCAGGTGGGTGGCCAAGATGGCGTCCCTGCACAACGCCACCCTGGTCCTCACCGTCGACCACAAGGG
CTGCGGCAACTACACCAGACTGCAGAAGGCCGTGGACGCCGTGCCCGACTACGCCGCGGCGCGCACGCTGATCGCCGTCG
ACGCGGGGGTGTACGCGGAGAAGGTGGTGGTGTGGAGCAACAAGACGGGCGTCACGCTGCAGGGCCGCGGCAACCTCAAC
ACCACCATCGTCTGGAACGACACCGCCAACTCCAGCGGCGGCACCTTCTACAGCGCCACCGTCGCCGTCCTCGCCGCCAA
CTTCGTGGCCTACAACGTCAGCGTCCAGAACACGGCTGCCCCCGCGGACCCGGGGGGCTCGGGCGGCCAGGCGGTGGCGC
TGCGCGTCGCCGGCGACCAGGCCGCCTTCTACTGGTGCGGCTTCTACAGCTCGCAGGACACACTGCTGGACGAGCAGGGC
CGCCACTTGTTCCGCGGCTGCTACGTCGAGGGCTCCATCGACTTCATCTTCGGCAACGCGCGCTCCCTCTACCTCGGCTG
CACCATCAGCTCCGTCGCCAACGCCGCCGCGGGCGGCACCGTCACGGGGAGCGTCACGGCGCACGGCCGCGCGTCGCCGG
CCGAGAAGACGGGCTTCGCGTTCGTGGGCTGCACCGTCGTGGGCACGGGGCAGGTGTGGCTGGGCAGGGCGTGGGGCCCC
TACGCCACCGTCGTCTTCGCCAGGACGTACCTCTCCGCTGTCGTCGCGCCCGGGGCATGGAACGACTGGAACGACCCCGC
CAGGCAGCAGTCGGTGTTCTTCGGGGAGTACGACTGCACGGGCCCCGGCGCCAGCGGTGGCACCGTGCAGAGGGTGGCCT
ACGCGAGGCAGCTGGACCAGCGCCAGGCCGCGCCATTCATGGACGTCTCCTACATCGACGGCAACCAGTGGGCGGTGCCC
CCTCTGCTTCCGCCCATGCAGGGCGCCGCCGGCGAGGACATCATCGTATCTGCTGAATTCAGTCATGGCCAGGCCGGCAT
CATGTAA

Alignment

ORF - retro_sbic_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.33 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVSIFCVDPNGCCEFTTVQAAVDAVPNHSSKRNVVWINKGIYFEKVTVPASKPNITFQGQGFDLTAIAWN
          A.....VD..GC...T..Q.AVDAVP.....R.......G.Y.EKV.V...K...T.QG.G...T.I.WN
Retrocopy ATLVLTVDHKGCGNYTRLQKAVDAVPDYAAARTLIAVDAGVYAEKVVVWSNKTGVTLQGRGNLNTTIVWN

Parental  DTAKSANGTFYSASVSVFASGFIAKNISFINVAPIPRPGAVDAQAVAIRINGDQAAFWGCGFFGAQDTLH
          DTA.S..GTFYSA.V.V.A..F.A.N.S..N.A....PG....QAVA.R..GDQAAF..CGF...QDTL.
Retrocopy DTANSSGGTFYSATVAVLAANFVAYNVSVQNTAAPADPGGSGGQAVALRVAGDQAAFYWCGFYSSQDTLL

Parental  DDRGRHYFKECFIQGSIDFIFGDARSLYENCRLISIADPVPSGQRSITGSVTAHARVSEDDNTGYSFVNC
          D..GRH.F..C...GSIDFIFG.ARSLY..C...S.A.....G....TGSVTAH.R.S....TG..FV.C
Retrocopy DEQGRHLFRGCYVEGSIDFIFGNARSLYLGCTISSVANAAAGG--TVTGSVTAHGRASPAEKTGFAFVGC

Parental  SIGGTGWIWLGRAWRPYSRVIFAYTSMSDIIASEGWNDWNDHTRDQTVFYGEYKCTGDGAN--LADRVPY
          ...GTG..WLGRAW.PY..V.FA.T..S...A...WNDWND..R.Q.VF.GEY.CTG.GA......RV.Y
Retrocopy TVVGTGQVWLGRAWGPYATVVFARTYLSAVVAPGAWNDWNDPARQQSVFFGEYDCTGPGASGGTVQRVAY

Parental  AQKLSDVQVLPYLNTSFIDGDQWLKP
          A..L...Q..P....S.IDG.QW..P
Retrocopy ARQLDQRQAAPFMDVSYIDGNQWAVP

Legend:

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

Expression

RNA-Seq

Sorghum bicolor was not studied using RNA-Seq expression data.

ChIP-Seq

Sorghum bicolor was not studied using ChIP-Seq data.

EST

Sorghum bicolor was not studied using EST data.

TSS

Sorghum bicolor was not studied using FANTOM5 data.

Lab

retro_sbic_44 was not experimentally validated.

Homology

Retrocopy orthology:

Sorghum bicolor 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA08G0054200	1 retrocopy	retro_ogla_15,
Oryza sativa japonica	OS08G0206950	1 retrocopy	retro_osat_13,
Sorghum bicolor	Sb07g006050	1 retrocopy	retro_sbic_44 ,