RetrogeneDB ID: retro_sbic_38

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 10:11930380..11932672(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb10g009880
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb10g005250
• Aliases: None
• Description: None

Sequence

>retro_sbic_38
ATGACGATCCTCTCGCCGCTCGCCACCAAGGTGTTCATCCCCGTCGCCGCCGTCATCGGCATCGTCTTCGCCGTCGTGCA
GTGGGTGCTCGTGTCGCGGGTGAAGCTCTCCCCGGCCGCGGCCGCCGCGTCCGGCGGAGGGAAGAACGGCTACGGCGACT
ACCTCATCGAGGAGGAGGAGGGGCTCAACGACCACAACGTCGTCGTCAAGTGCGCCGAGATCCAGAACGCTATCTCCGAA
GGAGCAACATCGTTTCTTTTCACTGAGTACCAATATGTTGGTATCTTCATGTCTATCTTCGCCGTTGTGATCTTCCTCTT
CCTTGGTTCGGTTGAGGGATTCAGCACGAAGAGCCAGCCCTGCACCTATAACAAGGACAAGTACTGCAAGCCTGCACTGT
TCACTGCCCTCTTCAGCACTGTGTCCTTCTTGCTTGGAGCCATCACCTCTCTGGTATCTGGTTTCCTTGGCATGAAGATT
GCCACATATGCGAATGCCAGAACTACCCTGGAAGCTAGGAAGGGTGTTGGCAAGGCTTTTATCACTGCTTTCCGCTCTGG
CGCTGTTATGGGTTTCCTGCTTGCATCAAGTGGGCTTGTGGTTCTGTACATCACCATTAATGTATTTAAGTTGTATTATG
GTGATGACTGGGAGGGTCTTTTTGAGTCTATCACTGGCTATGGCCTTGGTGGGTCGTCCATGGCTCTCTTCGGAAGAGTT
GGTGGAGGTATCTACACGAAGGCTGCTGATGTTGGTGCCGATCTTGTTGGAAAGGTCGAGAGGAACATTCCTGAGGATGA
TCCTAGGAACCCAGCTGTGATTGCTGATAATGTTGGTGACAATGTTGGTGACATTGCTGGAATGGGATCTGATCTCTTTG
GGTCATATGCTGAGTCTTCCTGTGCTGCCCTTGTTGTTGCGTCTATTTCATCTTTCGGAATCGACCATGACTTCACTGGG
ATGTGCTACCCACTCCTTGTTAGCTCTGTTGGTATCATCGTCTGCTTGATCACCACCCTTTTTGCTACTGATTTCTTTGA
AGTCAAGGCTGTGAAAGAAATTGAGCCCGCACTTAAGAAGCAGCTCATCATCTCCACCGCCCTAATGACTGTTGGTATTG
CTGTAATCAGCTGGTTGGCCCTTCCAGCTAAGTTCACCATCTACAACTTCGGTACTCAGAAGGATGTCTCCAACTGGGGC
TTGTTCTTCTGTGTTGCAATTGGTCTGTGGGCTGGTCTGATTATTGGTTTTGTCACAGAATACTACACTAGCAATGCATA
CAGTCCTGTGCAAGATGTCGCGGATTCGTGCAGAACCGGTGCTGCCACTAATGTCATTTTTGGTCTCGCTCTTGGATACA
AGTCAGTTATCATCCCGATTTTTGCTATCGCTGTTAGCATCTATGTCAGTTTCTCCATTGCTGCAATGTACGGCATCGCT
GTTGCCGCTCTTGGTATGCTGAGCACAATCGCAACTGGTCTTGCCATTGATGCTTATGGTCCCATCAGTGACAATGCTGG
TGGTATTGCTGAGATGGCTGGAATGAGCCACAGAATCTGTGAGAGAACTGATGCTCTTGATGCTGCTGGCAACACAACTG
CCGCTATTGGAAAGGGGTTTGCCATTGGTTCCGCTGCTCTTGTGTCCCTGGCGCTTTTTGGCGCCTTCGTCAGCAGAGCT
GGAGTGACGGTTGTCGATGTCCTCTCCCCCAAGGTTTTCATTGGTTTGATTGTTGGAGCCATGCTTCCCTACTGGTTCTC
TGCCATGACCATGAAGAGTGTTGGAAGTGCTGCCCTGAAGATGGTGGAGGAGGTCCGCAGGCAGCTCAACACCATTCCTA
GGTTGATGGAGGGAACTGCCAAGCCTGACTATGCAACCTGTGTGAAGATCTCCACCGATGCTTCCATCAAGGAGATGATT
CCCCCGGGTGCTCTGGTCATGCTCACTCCCCTCATTGTTGGAACCCTCATCGGTGTTGAGACTCTCTCTGGCGTTCTTGC
TGGTGCCCTGGTTTCTGGAGTGCAGATTGCCATCTCTGCTTCCAACACCGGTGGTGCATGGGACAATGCCAAGAAGTACA
TTGAGGCTGGTGCCAGCCAGCATGCAAGGACCCTCGGCCCCAAGGGATCTGACTGCCACAAGGCTGCTGTGATCGGTGAC
ACCATTGGTGACCCCCTGAAGGACACCTCGGGCCCGTCCCTCAACATCCTCATCAAGCTCATGGCCGTGGAGTCTCTTGT
GTTTGCCCCCTTCTTCGCCACCCAAGGTGGCATTCTGTTCAAGTACCTGTAA

Alignment

ORF - retro_sbic_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAILSPLATEVFIPVAAVIGIVFAVVQWVLVSRVKLSPTAAAASGGGKNGYGDYLIEEEEGLNDHNVVVK
          M.ILSPLAT.VFIPVAAVIGIVFAVVQWVLVSRVKLSP.AAAASGGGKNGYGDYLIEEEEGLNDHNVVVK
Retrocopy MTILSPLATKVFIPVAAVIGIVFAVVQWVLVSRVKLSPAAAAASGGGKNGYGDYLIEEEEGLNDHNVVVK

Parental  CAEIQNAISEGATSFLFTEYQYVGIFMSIFAVVIFLFLGSVEGFSTKSQPCTYSKDKYCKPALFTALFST
          CAEIQNAISEGATSFLFTEYQYVGIFMSIFAVVIFLFLGSVEGFSTKSQPCTY.KDKYCKPALFTALFST
Retrocopy CAEIQNAISEGATSFLFTEYQYVGIFMSIFAVVIFLFLGSVEGFSTKSQPCTYNKDKYCKPALFTALFST

Parental  VSFLLGAITSLVSGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGFLLASSGLVVLYITINVFK
          VSFLLGAITSLVSGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGFLLASSGLVVLYITINVFK
Retrocopy VSFLLGAITSLVSGFLGMKIATYANARTTLEARKGVGKAFITAFRSGAVMGFLLASSGLVVLYITINVFK

Parental  LYYGDDWEGLFESITGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAVIADNVGD
          LYYGDDWEGLFESITGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAVIADNVGD
Retrocopy LYYGDDWEGLFESITGYGLGGSSMALFGRVGGGIYTKAADVGADLVGKVERNIPEDDPRNPAVIADNVGD

Parental  NVGDIAGMGSDLFGSYAESSCAALVVASISSFGIDHDFTGMCYPLLVSSVGIIVCLITTLFATDFFEVKA
          NVGDIAGMGSDLFGSYAESSCAALVVASISSFGIDHDFTGMCYPLLVSSVGIIVCLITTLFATDFFEVKA
Retrocopy NVGDIAGMGSDLFGSYAESSCAALVVASISSFGIDHDFTGMCYPLLVSSVGIIVCLITTLFATDFFEVKA

Parental  VKEIEPALKKQLIISTALMTVGIAVISWLALPAKFTIYNFGTQKDVSNWGLFFCVAIGLWAGLIIGFVTE
          VKEIEPALKKQLIISTALMTVGIAVISWLALPAKFTIYNFGTQKDVSNWGLFFCVAIGLWAGLIIGFVTE
Retrocopy VKEIEPALKKQLIISTALMTVGIAVISWLALPAKFTIYNFGTQKDVSNWGLFFCVAIGLWAGLIIGFVTE

Parental  YYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYVSFSIAAMYGIAVAALGMLSTI
          YYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYVSFSIAAMYGIAVAALGMLSTI
Retrocopy YYTSNAYSPVQDVADSCRTGAATNVIFGLALGYKSVIIPIFAIAVSIYVSFSIAAMYGIAVAALGMLSTI

Parental  ATGLAIDAYGPISDNAGGIAEMAGMSHRIRERTDALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRA
          ATGLAIDAYGPISDNAGGIAEMAGMSHRI.ERTDALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRA
Retrocopy ATGLAIDAYGPISDNAGGIAEMAGMSHRICERTDALDAAGNTTAAIGKGFAIGSAALVSLALFGAFVSRA

Parental  GVTVVDVLSPKVFIGLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQFNTIPGLMEGTAKPDYATCVKI
          GVTVVDVLSPKVFIGLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQ.NTIP.LMEGTAKPDYATCVKI
Retrocopy GVTVVDVLSPKVFIGLIVGAMLPYWFSAMTMKSVGSAALKMVEEVRRQLNTIPRLMEGTAKPDYATCVKI

Parental  STDASIKEMIPPGALVMLTPLIVGTLFGVETLSGVLAGALVSGVQIAISASNTGGAWDNAKKYIEAGASE
          STDASIKEMIPPGALVMLTPLIVGTL.GVETLSGVLAGALVSGVQIAISASNTGGAWDNAKKYIEAGAS.
Retrocopy STDASIKEMIPPGALVMLTPLIVGTLIGVETLSGVLAGALVSGVQIAISASNTGGAWDNAKKYIEAGASQ

Parental  HARTLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNILIKLMAVESLVFAPFFATQGGILFKYL
          HARTLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNILIKLMAVESLVFAPFFATQGGILFKYL
Retrocopy HARTLGPKGSDCHKAAVIGDTIGDPLKDTSGPSLNILIKLMAVESLVFAPFFATQGGILFKYL

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_38 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	Sb10g005250	1 retrocopy	retro_sbic_38 ,