RetrogeneDB ID: retro_sbic_2

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:294751..295606(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g000490
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb10g000770
• Aliases: None
• Description: None

Sequence

>retro_sbic_2
ATGGTGCGCAAGGTGACCCTCAAGGTGATGGGTTGGATGTCCATCAGCGCGCTCTTGAGCATCGTCCTGGCCATGGGTCT
CCACTACTACGGCCTGCGCGCCACCACGGCCGCCATCTCCGTCAACTTCCTGAACCTGATCCCCGTGGCGACCTTCCTGA
TGGCTGTGCTGCTCCGCGTGGAGAAGCTGGCGGCGGGGACGTGGCCGGGGCGTGCGAAGATGGCCGGCACGGCCGTGTGC
GTGGGCGGCACCATGGTGGCCAGCCTGTACAGGGGCCCGCTGCTGCACCCGTGGCCGACGCACCTGCTCCGGCACCGCGC
CGCCACGGCGCCGCAGCACCACCGCAACATGCCGCTGGGCACCGTGTACCTGTGCGGCAGCTGCCTGGCCTACGCGCTCT
GGTTCGTCGTGCAGACGCGGGTGGGCAGGGTGTTCCCCTGCAAGTACCTGTCCACGATGCTGGCCTGCGTCTGCGGCACC
GTCCAGGCGCTCGCCATCGGCGCCGTCATCAGCAGGGGCGACCCGGCGTCGACGACGTGGCGGCTGTCGTGGGACCTCCG
CCTGGTCACCGTCGTCTACTCGGGGGTCTTCAACACCGCCGCCACCTTCTGCATCATCTCATGGGCCATCACCAGGCGAG
GCCCCATCTACCCGTCCATGTTCAACTCCCTCTCGCTCGTCGCAACCACCGTGCTCGACTCGCTGCTGCTCGGCACCGAC
GTCTCCGTCGGCAGCCTGCTCGGCGACGCGCTCATCATCCTCGGACTCTATGCCTTCCTCTGGGGAAAAGGCAGAGAGAT
GAAGCACCTCAAACAACAACAAGAGCAGCAGCAGCTCAACGGGACGGGACCATGA

Alignment

ORF - retro_sbic_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.64 %
• Parental protein coverage: 93.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLYYYGLQVTSAAYSVVFLNLIPIVTFAIAILVRAEKVALGKWPSRLKVLGALTCVGGTMIVSLLKGHL
          MGL.YYGL..T.AA.SV.FLNLIP..TF..A.L.R.EK.A.G.WP.R.K..G...CVGGTM..SL..G.L
Retrocopy MGLHYYGLRATTAAISVNFLNLIPVATFLMAVLLRVEKLAAGTWPGRAKMAGTAVCVGGTMVASLYRGPL

Parental  LHLWPTHLLKLSHGSAPASGGHHHDMLTGTLFLSGSCLSYAVWFIVQARVGKVFPSMYWGTMLTCLLGSI
          LH.WPTHLL......AP....HH..M..GT..L.GSCL.YA.WF.VQ.RVG.VFP..Y..TML.C..G..
Retrocopy LHPWPTHLLRHRAATAPQ---HHRNMPLGTVYLCGSCLAYALWFVVQTRVGRVFPCKYLSTMLACVCGTV

Parental  QAFVVSLFLSHD---RADWRLKWDLQLLTVVYSGVLNTGINFVLISWAVSRRGPIYPSMFNSLSLIITVV
          QA.......S........WRL.WDL.L.TVVYSGV.NT...F..ISWA..RRGPIYPSMFNSLSL..T.V
Retrocopy QALAIGAVISRGDPASTTWRLSWDLRLVTVVYSGVFNTAATFCIISWAITRRGPIYPSMFNSLSLVATTV

Parental  MDSLLLGTKIYVGGVVGALLIIVGLYAFLWGKGKELQAAAAEKKKK
          .DSLLLGT...VG...G..LII.GLYAFLWGKG.E...........
Retrocopy LDSLLLGTDVSVGSLLGDALIILGLYAFLWGKGREMKHLKQQQEQQ

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_2 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	Sb10g000770	1 retrocopy	retro_sbic_2 ,