RetrogeneDB ID: retro_sbic_36

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:68793224..68794220(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g041250
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb06g026100
• Aliases: None
• Description: None

Sequence

>retro_sbic_36
ATGTTTTACGGGGGATATGCTTACCATCGCAACTCGTTTGCGCAAATCTACCGTTGTTATCCACCATCCTTTGTTGGTAA
GCCACACCTAGAAGGCGGTGACAAAGTAATAATGCCACAGTCTGCCCTTGATTGTCTTGCTTCCTTGCACATCGAGTACC
CTATGCTCTTCGAGTTCGAGCTGCACAACGATGCTGCTGCTACCCAGCAGCGGGTTTCACACTGTGGCGTTCTGGAGTTC
GTAGCGGAAGAAGGCATGATCATCATGCCCTACTGGATGATGCAGAACATGCGTCTTGAAGAGGGCGACATCGTCCATGT
CAAGAACGCGGCTCTTCCCAAGGGAACATATGCGAAACTGCAGCCTCACACGAGTGATTTCCTGGACATCTCAAACCCGA
AGGTCGTCTTGGAAAAGACTCTGAGGAATTTCTCCTGCTTAACCACGGGAGACACCATCATGGTATCCTACAACAGCAAA
CAGTATTACATCGATATCGTTGAAACAAAGCCTGCTTCAGCAGTTTGCATTATTGAGACAGACTGTGAAGTGGACTTTGC
ACCTCCTCTTGATTATAAAGAACCTGCTGAGAAACCACGGCAATCAACAGTTCTTCCTGCAAGCAACAAGGCACCTGCGG
CTGGAGATGGCAACACTACTGCTGTGGAGGATGAACCGAAATTCAAACCATTTACTGGTTCTGGAAAGCGGTTGGATGGA
AAGGCCTCAAAACTGCAAGCATCTGATCAGGTTCCTAACACTGCAATTTCTGCACCTTCAGGTTCAAACAAAAGAGCAAA
TCAGCAAATCTCGGCACCGGCAGCTTCAGTAGGTAGCAATTACAGTCGACAGAAAGCTGGAAAGCTTGTTTTTGGTTCAA
GTGCAAGCAACAATAAGCAACTACAAAAGGCTCCTGCTAAAGAGGAGGAACCCACGAAAAAGGACGAGCCCAGGTTCCAA
GCGTTCAGTGGGAAGAGCTACTCATTGAAACGTTAG

Alignment

ORF - retro_sbic_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFYGGYAYHGNSFEQTYRCYPASFFDKPHLEGGDKVIMPPSALDRLASLHIEYPMLFE--LHNDAT---Q
          MFYGGYAYH.NSF.Q.YRCYP.SF..KPHLEGGDKVIMP.SALD.LASLHIEYPMLFE..LHNDA....Q
Retrocopy MFYGGYAYHRNSFAQIYRCYPPSFVGKPHLEGGDKVIMPQSALDCLASLHIEYPMLFEFELHNDAAATQQ

Parental  RISHCGVLEFVAEEGMIIMPYWMMQNMLLQEGDTVHVKNATLPKGTYVKLQPHTTDFLDISNPKAILEKT
          R.SHCGVLEFVAEEGMIIMPYWMMQNM.L.EGD.VHVKNA.LPKGTY.KLQPHT.DFLDISNPK..LEKT
Retrocopy RVSHCGVLEFVAEEGMIIMPYWMMQNMRLEEGDIVHVKNAALPKGTYAKLQPHTSDFLDISNPKVVLEKT

Parental  LRNFSCLTTGDSIMVAYNNKQYYIDIVETKPASAVSIIETDCEVDFAPPLDYKEP-EKPRQPTV--PAGK
          LRNFSCLTTGD.IMV.YN.KQYYIDIVETKPASAV.IIETDCEVDFAPPLDYKEP.EKPRQ.TV.....K
Retrocopy LRNFSCLTTGDTIMVSYNSKQYYIDIVETKPASAVCIIETDCEVDFAPPLDYKEPAEKPRQSTVLPASNK

Parental  APAE-DGN-TVVEDEPKFKPFTGSGKRLDGKASKLQSS-VGPSTALSAPSDSNKRGNQQMSAPAASGASN
          APA..DGN.T.VEDEPKFKPFTGSGKRLDGKASKLQ.S...P.TA.SAPS.SNKR.NQQ.SAPAAS..SN
Retrocopy APAAGDGNTTAVEDEPKFKPFTGSGKRLDGKASKLQASDQVPNTAISAPSGSNKRANQQISAPAASVGSN

Parental  YSRQKTGKLVFGSSASNNKEPQKAPVKEEEPAKKDEPRFQAFSGKSYSLKR
          YSRQK.GKLVFGSSASNNK..QKAP.KEEEP.KKDEPRFQAFSGKSYSLKR
Retrocopy YSRQKAGKLVFGSSASNNKQLQKAPAKEEEPTKKDEPRFQAFSGKSYSLKR

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_36 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA016968	1 retrocopy	retro_oind_28,
Sorghum bicolor	Sb06g026100	1 retrocopy	retro_sbic_36 ,