RetrogeneDB ID: retro_sbic_37

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:11368682..11371823(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g010540
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g022460
• Aliases: None
• Description: None

Sequence

>retro_sbic_37
ATGGCGACCGATGGGCAGCTCAGGGAGTGGGTCTCCGACAAGCTCATGAGCCTCTTGGGCTACTCCAAGAACGTCGTCGT
CCAGTACGTCATCAGGCTCGCGAAGGAGTGCTCTTCAACGGGTGACCTCGTGGGTAAGCTCGTCGAGTTCGGGTTCACCT
CGTCTGCGGAGACCCGTGCCTTCGCGTCGGATGTCTACGCCAAGGTTCCCCGCAGGGCCAGCGGCATCAGTAATTACCAG
AAGCAGGAGAGGGAGGCGGCAAAGCTTGCCCAGAAACAGAGCACTTACAAGCTGTTGGCCAACGAGGATGATGATACCGA
CAACCAGACACCAACAAGTCAAAAGACCTCAAGAAATCCATCATCTAAGAGTCGGAAGCATTTCAGGAGGAAAGCAGATC
AAGACAGTGGTGATGATGAAATAGTGGCAAAAGATTCTGGAAGGAACGTCCGTCAGCGAACAGAAGAGGAGGATGAAGAA
AGTGGCGATGGAAGTTCTGATGAAGAGAAAGAAAGGATTAGAGATCAGCAGGAAAAGGCCCAGCTAGAAAGGAACATGAG
AGAAAGAGATGCGGCTAACACAAGGAAGTTGATGGAGCGACAATTATCTAAGGAAGAACAAGAAGAGCTTACTAGAAGAT
CTCAAGCAATGGACAAGAATGACACATCTGATCTGAGAAAATTCTCAAGGCAAGCATACCTGCAAAAGCGCCGGGACAAA
AAAATTGAGGAAATTCGTGATGAAATTCTGGACCACCAGTACATTTTTCAGGATGTGAAACTAACAGAGGCAGAAGAAAA
GGAGTTGAGATACAAGATGAAGATATATGATCTTGTCAAGGAACATGTTGAGACTCCTGATGATGTTGGTGAGTACAAAA
TGCCTGAAGCTTATGACATGGGTGAAAATGTCAATCAAGAAAAGAGATTCTCTGTGGCCATGCAGCGGTACAAAGATCCT
GAGGCCAAGGATAAAATGAACCCTTTTGCTGAACAGGAAGCGTGGGGAGAACACCAAATAGGAAAATCGAAACTGCAATT
TGGATCCAAAGATAAGAAGCCGTCTTCAGATGAGTATCAGTATGTATTCGAAGATACAATTGATTTTGTTAAATCATCAG
TCATAGTAGGAACCCAGCCTGAAGACGATTCAGATAAAGAGGACATTGAAGCAAAAGATATTTTGAAAAGGGAGCTCCAG
GATGAGCGAAAGACGCTTCCAGTTTTCAAATTTGGGGATGAACTGCTTAAGGCTGTAGAAGAGTATCAGGTTATCGTCAT
AGTGGGCGAGACCGGGTCCGGTAAAACAACACAAATACCTCAGTACCTTCATGAGGCTGGGTATACTGCGAAAGGAAAGG
TTGCATGTACTCAACCTCGTCGAGTGGCTGCCATGAGTGTTGCAGCAAGAGTATCTCAAGAAATGGGTGTTAAACTTGGA
CATGAGGTTGGTTACTCTATAAGATTTGAGGATTGCACTTCAGATAAAACAATTATTAAGTACATGACTGATGGAATGCT
TCTAAGGGAGTTCCTTGGTGAACCAGATTTGGCTAGCTACAGTGTTGTCATGGTGGATGAGGCTCATGAGCGTACCCTTT
CCACGGATATCTTATTTGGTCTGGTGAAGGATATTTCTCGTTTTCGACCAGACCTGAAGTTGCTCATTTCGAGTGCCACG
CTTGATGCAGAAAAATTTAGTGACTACTTCGATTCAGCTCCTATTTTCAAGATACCTGGGAGGCGATACCCTGTTGAAAT
TCATTATACAAAAGCCCCAGAGGCTGATTACATAGATGCAGCAATTGTCACTGTTTTACAGATACATGTGACACAACCCC
CTGGAGATATCCTGGTGTTTCTTACAGGTCAGGAGGAAATTGAAACAGTTGATGAAATCCTTAAACACAGAACAAGGGGC
TTAGGCACCAAAATTTCAGAATTAATTATATGTCCTATTTATGCAAATCTGCCTACCGAGCTTCAAGCTAAGATATTTGA
GCCAACCCCCGAGGGTGCCCGTAAGGTGGTTCTGGCCACTAATATAGCTGAGACTTCACTAACCATTGATGGTATAAAGT
ATGTTATTGATCCAGGCTTTTGTAAGATCAAATCATACAATCCCCGCACAGGAATGGAATCTCTACTTATTAATCCTATC
TCAAAAGCTTCAGCAAACCAGAGGGCAGGAAGGTCTGGACGCACTGGACCTGGAAAATGCTTCCGTCTATACACGAGTTA
TAACTACATGCACGACCTAGAAGATAATACTGTTCCAGAGATCCAACGAACCAATCTTGCGAATGTTGTGCTTACACTCA
AGAGTCTTGGTATTCATGACTTGGTTAACTTTGACTTCATGGATCCACCTCCATCAGAAGCCCTGTTAAGGGCTCTGGAA
CAACTTTTTGCTCTCAGTGCACTCAACAGTCGTGGAGAGTTGACTAAGACTGGAAGAAGAATGGCAGAATTTCCACTGGA
TCCTATGTTGTCGAAGATGATTGTTGCTTCAGAGAAATATAAGTGTTCTGATGAGATCATCTCCGTTGCATCCATGTTGT
CAATTGGCAATTCTATATTTTATCGTCCGAAGGACAAACAAGTTCATGCAGATAATGCAAGGTTGAACTTCCACACTGGC
AATGTTGGGGACCATATAGCACTACTAAATGTGTATAATTCTTGGAAAGAAACAGACTATTCGACTCAGTGGTGTTATGA
AAACTATATACAGGTGCGCAGCATGAAGAGGGCAAGGGATATTCGGGATCAACTAGAGGGGCTTATGGAAAGAGTTGAGA
TTGAGATTTGCTCAAATGCCAGTGATTTAGATGCTATTAAAAAAGTTATAACATCAGGTTTCTTCCATCATTCTGCACGG
TTGCAGAGGGATGGTACATATAAGACTGTCAAGAACCCTCAGACCGTACATATCCATCCTAGTTCAGGATTAGCAGAGAT
ACGTCCGCGGTGGGTAGTATACCACGAATTAGTTCTCACAACAAAGGAGTTTATGCGCCAGGTGACAGAACTGAAGCCTG
AATGGCTGGTAGAGATAGCACCACATTATTACCAACTAAAGGATGTGGAAGACTCTGGAACAAAGAAGCTACCAAAGGGC
CAAGGACGAGCTGCATTGTAG

Alignment

ORF - retro_sbic_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.1 %
• Parental protein coverage: 62.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EELTRRSQAMDKNDTSDLRKFSRQAYLQKRRDKKIEEIRDEILDHQYIFQDVKLTEAEEKELSYKMKLYG
          EELTRRSQAMDKNDTSDLRKFSRQAYLQKRRDKKIEEIRDEILDHQYIFQDVKLTEAEEKEL.YKMK.Y.
Retrocopy EELTRRSQAMDKNDTSDLRKFSRQAYLQKRRDKKIEEIRDEILDHQYIFQDVKLTEAEEKELRYKMKIYD

Parental  LVKEHVETPDDVGEYKMPEAYDMGENVNQEKRFSVAMQRYKDPEAKDKMNPFAEQEAWEEHQIGKSKLRF
          LVKEHVETPDDVGEYKMPEAYDMGENVNQEKRFSVAMQRYKDPEAKDKMNPFAEQEAW.EHQIGKSKL.F
Retrocopy LVKEHVETPDDVGEYKMPEAYDMGENVNQEKRFSVAMQRYKDPEAKDKMNPFAEQEAWGEHQIGKSKLQF

Parental  GSKDKKTSSDEYQYVFEDTIDFVKSSVIEGTQPEDDSDKEDVEAKDILKRELQDERKTLPIFKFRDELLK
          GSKDKK.SSDEYQYVFEDTIDFVKSSVI.GTQPEDDSDKED.EAKDILKRELQDERKTLP.FKF.DELLK
Retrocopy GSKDKKPSSDEYQYVFEDTIDFVKSSVIVGTQPEDDSDKEDIEAKDILKRELQDERKTLPVFKFGDELLK

Parental  AVEEYQVIVIVGETGSGKTTQIPQYLHEAGYTAKGKVACTQPRRVAAMSVAARVSQEMGVKLGHEVGYSI
          AVEEYQVIVIVGETGSGKTTQIPQYLHEAGYTAKGKVACTQPRRVAAMSVAARVSQEMGVKLGHEVGYSI
Retrocopy AVEEYQVIVIVGETGSGKTTQIPQYLHEAGYTAKGKVACTQPRRVAAMSVAARVSQEMGVKLGHEVGYSI

Parental  RFEDCTSDKTIIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVKDISRFRPDLKLLIS
          RFEDCTSDKTIIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVKDISRFRPDLKLLIS
Retrocopy RFEDCTSDKTIIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVKDISRFRPDLKLLIS

Parental  SATLDAEKFSDYFDSAPIFKIPGRRYPVEIHYTKAPEADYIDAAIVTVLQIHVTQPPGDILVFLTGQEEI
          SATLDAEKFSDYFDSAPIFKIPGRRYPVEIHYTKAPEADYIDAAIVTVLQIHVTQPPGDILVFLTGQEEI
Retrocopy SATLDAEKFSDYFDSAPIFKIPGRRYPVEIHYTKAPEADYIDAAIVTVLQIHVTQPPGDILVFLTGQEEI

Parental  ETVDEILKHRTRGLGTKISELIICPIYANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVID
          ETVDEILKHRTRGLGTKISELIICPIYANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVID
Retrocopy ETVDEILKHRTRGLGTKISELIICPIYANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVID

Parental  PGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMHDLEDNTVPEIQRTNLA
          PGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMHDLEDNTVPEIQRTNLA
Retrocopy PGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMHDLEDNTVPEIQRTNLA

Parental  NVVLTLKSLGIHDLVNFDFMDPPPSEALLRALEQLFALSALNSRGELTKTGRRMAEFPLDPMLSKMIVAS
          NVVLTLKSLGIHDLVNFDFMDPPPSEALLRALEQLFALSALNSRGELTKTGRRMAEFPLDPMLSKMIVAS
Retrocopy NVVLTLKSLGIHDLVNFDFMDPPPSEALLRALEQLFALSALNSRGELTKTGRRMAEFPLDPMLSKMIVAS

Parental  EKYKCSDEVISIASMLSIGNSIFYRPKDKQVHADNARLNFHTGNVGDHIALLNVF
          EKYKCSDE.IS.ASMLSIGNSIFYRPKDKQVHADNARLNFHTGNVGDHIALLNV.
Retrocopy EKYKCSDEIISVASMLSIGNSIFYRPKDKQVHADNARLNFHTGNVGDHIALLNVY

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_37 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 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37 ,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,