RetrogeneDB ID: retro_sbic_48

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 1:73435603..73436965(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb01g050390
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g029510
• Aliases: None
• Description: None

Sequence

>retro_sbic_48
ATGGCCATGCCGCCGCCGCGCTCTCTCCGCGTCGCCGTCATCGGTGCGGGAGCCGCGGGGCTGGCCGCCGCGCGCGAGCT
GCGGCGCGAGGGCCACGCGACCGTCGTGTTCGAGCGCGGCCACGCAGTCGGGGGCACCTGGCTCTACGACCACCGCAGCA
GCAGCATGTACGCGTCCCTGCGCACCAACCTGCCACGCGAGATCATGGGCTTCCTCGACTTCCCCTTCGCCGCCGCTTCG
GACTCCGTCGACGCGCGCAGGTTCCCTCGCCACCAGGAGGTGCTGCGCTACATCCAGGCCTTCGCGCGCCGGTTCCACCT
TGACGGCCTCGTCCGCCTCCGCACGGAGGTGCTCGCCGTCACCACCAAGGACGACGACGAGGGGAGCAGCTGGAGGGTGA
GGTGGCGCCGGAACGCAGCCGCCGCCGGTGAGCAGGAGGAGGAGGAGGAGGAGGTGTTCGACGCCGTCGTGGTCTGCAAC
GGCCACTACACGGAGCCGCGAACCGCCGCCGACGACATCCCCGGCCTGGACGCCTGGCCGCCGGGCAAGCAGATGCACAG
CCACAGCTACCGCGTGCCGGGCCCGTTCGCGGACCAGGTCGTGGTCATAGTCGGTGCCAGCAACAGCGGCGCCGACATCT
CCAGGGAAATCGCCGGCGTGGCCAGGGAGGTGCACATGGCCGACAGATGGGCCCCCGCCGCCACCTGCCGGAGGCTCCCC
GGCTATCGCAACCTCTGGCTCCGCTCCATGGTGGAGCGTGCCGACGCGGACGGCACCACCGTCGTGTTCCGAGACGGCAG
CTCCGTCAGAGCGGACGTCGTCATGCACTGCACCGGATACAAGTACAGCTTCCCCTTCCTCCTGACGGCGGCGGGCGATG
GCGATACCGCGGTCGTCTCCGTGGATGACAACCGCATCCACCCGCTGTACAAGCACGTGTTCGTGCCTCAGCTGGCTCCC
CACCTCGCCTTCATCGGCCTGCCCTTCAAGGTGATCCCGTTCCCGATGTTCCAGCTGCAGGCCAGCTGGGTCGCCGGCGC
TCTGTCGGGCCGGATCCAGCTCCCGTCGGAGGAGGAGATGATGGAAGACGTGAGGGCGCTTTACTCGGAGCTGGAGGTCA
TGGGATGGCCCGTCAGGTACACGCACTGCATGAAGCACAGCCAGTTCGAGTACGACGAGTGGCTGGCGGAGCAGTGCCAG
TGCGGCGGGGAAGCCGGCACACGCACAGTGGAGGAGTGGAGGAAGGACATGTTCAACGCCACCAGGAAGAAGAAGCTCCA
GTGCCCGGAGACGTACAGAGACGAGTGGGACGATCACCATTTGCTGGAACAAGCGTACCAAGACTTCAACAATTACTTGT
AA

Alignment

ORF - retro_sbic_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.0 %
• Parental protein coverage: 75.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSLYASLRTNLPRETMGFLDFPFAAGAAAAGSPRDPRRFPGHEEVLRYLEAFARRFDLLRLVRFETEVLS
          SS.YASLRTNLPRE.MGFLDFPF....AAA....D.RRFP.H.EVLRY..AFARRF.L..LVR..TEVL.
Retrocopy SSMYASLRTNLPREIMGFLDFPF----AAASDSVDARRFPRHQEVLRYIQAFARRFHLDGLVRLRTEVLA

Parental  VR-REDGGGGRWAVTSRK----LGEKGSGQEEFYDAVVVCNGHYTEPRIAV--IPGVDAW-PGKQMHSHN
          V....D..G..W.V..R......GE.....EE..DAVVVCNGHYTEPR.A...IPG.DAW.PGKQMHSH.
Retrocopy VTTKDDDEGSSWRVRWRRNAAAAGEQEEEEEEVFDAVVVCNGHYTEPRTAADDIPGLDAWPPGKQMHSHS

Parental  YRVPEPFLDQVVIVIGASASAFDISRDIASMAEEVHIADRSAPASTCKKEPGYDNLWLHSMIDHAQEDG-
          YRVP.PF.DQVV...GAS.S..DISR.IA..A.EVH.ADR.APA.TC...PGY.NLWL.SM...A..DG.
Retrocopy YRVPGPFADQVVVIVGASNSGADISREIAGVAREVHMADRWAPAATCRRLPGYRNLWLRSMVERADADGT

Parental  TVVFQDGSSIKADVIMHCTGYLYDFPFL----GDDST--ITVDDNRVDPLYKHIFPPEVAPHLSFIGLPW
          TVVF.DGSS..ADV.MHCTGY.Y.FPFL....GD..T....VDDNR..PLYKH.F.P..APHL.FIGLP.
Retrocopy TVVFRDGSSVRADVVMHCTGYKYSFPFLLTAAGDGDTAVVSVDDNRIHPLYKHVFVPQLAPHLAFIGLPF

Parental  KVIPFPLFELQSKWVARVLSGRVKLPSKDKMMEDVKAFYLKLEALGWPKRYTHNFSNHQFEYDDWLAEQC
          KVIPFP.F.LQ..WVA..LSGR..LPS...MMEDV.A.Y..LE..GWP.RYTH.....QFEYD.WLAEQC
Retrocopy KVIPFPMFQLQASWVAGALSGRIQLPSEEEMMEDVRALYSELEVMGWPVRYTHCMKHSQFEYDEWLAEQC

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_48 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sorghum bicolor	Sb01g029510	1 retrocopy	retro_sbic_48 ,