RetrogeneDB ID: retro_sbic_7

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 1:21751860..21753503(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb01g019850
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g047500
• Aliases: None
• Description: None

Sequence

>retro_sbic_7
ATGGCCTTCAACCTGGCTCAGTGCGCCACCGCTGCGGCGTCCGTCGCGCCCCGCACCCCTCGCCCTGCTAGGTCCGCGGT
CGCGGCGTCCGTGTCTGTCTCCACAAGGAAGGCGGCGGACGGCAGGCTGCGGCTGCAGCGGCAGGCGAGCTGCGAGCCGT
CGGTGGCGCCGTCGCGTTCGGTGTTCTGCCGGGCCGCGGTGTCGGGGAAGAGCGCGGCCGACCGGGCCGCCTCCACCAGG
AGGAGGTCCGGCGTGCCGGTGTTCGTCATGATGCCGCTGGACACCGTGAAGAAGTGCGGCAGCGCGCTGAACCGCCGCAA
GGCGGTGCAGGCGAGCCTGTCCGCGCTCAAGAGCGCGGGCGTGGAGGGCATCATGGTGGACGTGTGGTGGGGCATCGCCG
AGAGCGACGGCCCCGGGAGGTACAACTTCGCGGGGTACATGGAGCTCATGGAGATGGCGCGCAAGGCCGGGCTCAAGGTG
CAGGCCGTCATGTCCTTCCACCAGTGCGGCGGCAACGTCGGCGACTCCGTCAACATCCCGCTGCCGCGGTGGGCCGTGGA
GGAGATGGAGAAGGACCAGGACCTCTGCTACACCGACCAGTGGGGCCGACGCAACTACGAGTACGTCTCCCTCGGCTGCG
ACGCCATGCCCGTCCTCAAGGGCCGCACCCCCGTCGAGTGCTACACCGACTTCATGCGCGCGTTCCGGGACCACTTCGCC
GACTACCTCGGCAACACCATCGTGGAAATCCAGGTCGGCATGGGCCCCGCCGGCGAGCTGCGCTACCCGTCGTACCCGGA
GAGCAACGGCACCTGGAAGTTCCCCGGCATCGGCGCCTTCCAATGCAACGACAGGCACATGCGTAGCAGCCTGAAGGCGG
CGGCGGAGGCGGCCGGCAAGCCGGAGTGGGGCCACGGTGGCCCCACGGACGCTGGCGGCTACAACAACTGGCCCGAGGAC
ACCCTCTTCTTCCGCGCCGACAACGGCGGGTGGAGCACCCAGTACGGCGACTTCTTCCTGTCGTGGTACTCGCAGATGCT
GCTGGAGCACGGCGACCGCATCCTGTCGGGCGCCACGTCCGTGTTCGGCGCGTCGTCGCCCGTGGAGGTGTCCGTGAAGG
TGGCCGGCATCCACTGGCACTACGGCACCCGGTCGCACGCGCCGGAGCTGACCGCGGGGTACTACAACACGCGGCACCAC
GACGGGTACCGCCCCATCGCGGACCTCCTGGCCCGCCACGGCGCCGTGCTCAACTTCACCTGCGTGGAGATGCGGGACCA
CGAGCAGCCGCAGGAGGCGCAGTGCATGCCGGAGCACCTGGTCCGGCAGGTGGGCGCCGCGGCGCGCGCAGCGGGCGTGG
GCCTCGCGGGCGAGAACGCGCTGCCCAGGTACGACGGCACGGCGCACGACCAGGTGGTAGCCACCGCCGCGCAGCGCGCC
GCCGAGGACCGGATGGTGGCGTTCACGTACCTGCGCATGGGGCCCGACCTCTTCCACCCGGACAACTGGCAGCGGTTCGC
CGCCTTCGTGCGCCGCATGAACGGCGCCGGGTCGTGCCGGGAGGCCGCGGAGCGGGAGGCGCACGGCGTCGCGCAGGCAA
CCGGGTCGCTGGTGCACGAGGCCGCCGTCGCGCTGCGGAGCTG

Alignment

ORF - retro_sbic_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 84.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADVAAELKTKAGVPVFVMMPLDTVRKDGNSLNRRKAVEASLAALKSAGVEGIMVDVWWGIAEADGPGQYN
          AD.AA......GVPVFVMMPLDTV.K.G..LNRRKAV.ASL.ALKSAGVEGIMVDVWWGIAE.DGPG.YN
Retrocopy ADRAASTRRRSGVPVFVMMPLDTVKKCGSALNRRKAVQASLSALKSAGVEGIMVDVWWGIAESDGPGRYN

Parental  FNGYMELMEMARKTGLKVQAVMSFHQCGGNVGDSVTIPLPRWVVEEMDKDQDLAYTDRSGRRNYEYVSLG
          F.GYMELMEMARK.GLKVQAVMSFHQCGGNVGDSV.IPLPRW.VEEM.KDQDL.YTD..GRRNYEYVSLG
Retrocopy FAGYMELMEMARKAGLKVQAVMSFHQCGGNVGDSVNIPLPRWAVEEMEKDQDLCYTDQWGRRNYEYVSLG

Parental  CDTLPVLKGRTPIQCYADFMRAFRDHFATFMGNTIVEIQVGMGPAGELRYPSYPESDGTWSFPGIGEFQC
          CD..PVLKGRTP..CY.DFMRAFRDHFA...GNTIVEIQVGMGPAGELRYPSYPES.GTW.FPGIG.FQC
Retrocopy CDAMPVLKGRTPVECYTDFMRAFRDHFADYLGNTIVEIQVGMGPAGELRYPSYPESNGTWKFPGIGAFQC

Parental  YDRYMLSSLKAAAESVGKPEWGNGGPGDAGGYKNWPEDTGFFRRE-GGWSNEYGQFFMSWYSQMLLEHGE
          .DR.M.SSLKAAAE..GKPEWG.GGP.DAGGY.NWPEDT.FFR...GGWS..YG.FF.SWYSQMLLEHG.
Retrocopy NDRHMRSSLKAAAEAAGKPEWGHGGPTDAGGYNNWPEDTLFFRADNGGWSTQYGDFFLSWYSQMLLEHGD

Parental  RILSAATGVYTGSPGVKISVKVAGIHWHYGTRSHAAELTAGYYNTRHHDGYAPIARMLARHGAVLNFTCV
          RILS.AT.V...S..V..SVKVAGIHWHYGTRSHA.ELTAGYYNTRHHDGY.PIA..LARHGAVLNFTCV
Retrocopy RILSGATSVFGASSPVEVSVKVAGIHWHYGTRSHAPELTAGYYNTRHHDGYRPIADLLARHGAVLNFTCV

Parental  EMRDHEQPQDAQCRPEALVQQVAAAAREAGVGLAGENALPRYDETAHDQVVATAADRAAEDRMVAFTYLR
          EMRDHEQPQ.AQC.PE.LV.QV.AAAR.AGVGLAGENALPRYD.TAHDQVVATAA.RAAEDRMVAFTYLR
Retrocopy EMRDHEQPQEAQCMPEHLVRQVGAAARAAGVGLAGENALPRYDGTAHDQVVATAAQRAAEDRMVAFTYLR

Parental  MGPDLFQPDNWRRFAAFVKRMSQPGARDACREQVEREADGVAHATQPLVHEAAVAL
          MGPDLF.PDNW.RFAAFV.RM...G....CRE..EREA.GVA.AT..LVHEAAVAL
Retrocopy MGPDLFHPDNWQRFAAFVRRMNGAG---SCREAAEREAHGVAQATGSLVHEAAVAL

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_7 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	Sb01g047500	1 retrocopy	retro_sbic_7 ,