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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAACGCCCCGCCGCGGCGATGGGGTGCTTCCATTCCACGGCGAAGCGGCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgccaatcccattccttgccatacgcatacgagctactcgcgtgagttccttttttttcttatttagtttcaatgattgccgttgttggaatg...

Basic information

species Zea mays
transcript GRMZM2G107575_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107575_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g41510.1 (Oryza sativa), 5'ss of exon 1
-AGGAAACGCCCCGCCGCGGCGATGGGGTGCTTCCATTCCACGGCGAAGCGGCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgccaatcccattccttgccat---acgcatacgagctactcgcgtgagttccttttttttcttatttagtttcaatgattgccgttgttggaatg---------------------------------------
  ||    |   ||| | || ||||||||||||||| || ||||||| ||| |  | ||| || ||||||||||||||   |||||||||| |||||||||||||||| |    | |  | | ||||||    | |  |||     | |   ||   |   ||  |||  | |  |||||    |||||   |   | |    |                                       
CTGGGCGGGGTGCGC-GTGGGGATGGGGTGCTTCCAGTCGACGGCGAGGCGTCCGCGCCCGGGGTACGAGGACCCCGTCGGCCTCGCCTCCGAGACCGCCTgtgagtt-gttgttgctgtac-ttgccacttgaggagtactctacagtactgtatttcatttcatttcatcaagtagttcatctgatttatgcaatcgatgggcgtactggaaattctgagttagttgttttggatgtgtag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86466680|gb|DY233050.1|DY233050
EST:     CCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: CCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|86468277|gb|DY234647.1|DY234647
EST:     GCAACACCCTGGTTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAACATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|149079633|gb|EE168627.2|EE168627
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211199939|gb|FL305450.1|FL305450
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAG
EST: gi|101388735|gb|EB816351.1|EB816351
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|91053272|gb|EB163690.1|EB163690
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|32799975|gb|CD952211.1|CD952211
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|71320554|gb|DR797018.1|DR797018
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGTCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|78085933|gb|DV514326.1|DV514326
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|32804727|gb|CD956963.1|CD956963
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211199934|gb|FL305445.1|FL305445
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|149016909|gb|EE045638.2|EE045638
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211202489|gb|FL305452.1|FL305452
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211199937|gb|FL305448.1|FL305448
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|76018012|gb|DT945182.1|DT945182
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|71427887|gb|DR808937.1|DR808937
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|32799514|gb|CD951750.1|CD951750
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|20208081|gb|BQ134170.1|BQ134170
EST:     GCTTTACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211202488|gb|FL305451.1|FL305451
EST:     GCAACACCCTGGCTACGAGGACCCTGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATT
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATT
EST: gi|211199935|gb|FL305446.1|FL305446
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTC
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTC
EST: gi|211199936|gb|FL305447.1|FL305447
EST:     GCAACACCCTGGCTACGAAGACCCCGTGCACCTCGCCTCCCAGAACGCCT                         TCAGCGTTAGTGAGGTTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTG
EST: gi|32809691|gb|CD961925.1|CD961925
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGTCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211199933|gb|FL305444.1|FL305444
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|211199938|gb|FL305449.1|FL305449
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|26456204|gb|CA827787.1|CA827787
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|91052665|gb|EB163083.1|EB163083
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
EST: gi|71317611|gb|DR795553.1|DR795553
EST:     GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCT                         TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG
genomic: GCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 64

AGGAAACGCCCCGCCGCGGCGATGGGGTGCTTCCATTCCACGGCGAAGCGGCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 60

AGGAAACGCCCCGCCGCGGCGATGGGGTGCTTCCATTCCACGGCGAAGCGGCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

AGGAAACGCCCCGCCGCGGCGATGGGGTGCTTCCATTCCACGGCGAAGCGGCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

AGGAAACGCCCCGCCGCGGCGATGGGGTGCTTCCATTCCACGGCGAAGCGGCAACACCCTGGCTACGAGGACCCCGTGCACCTCGCCTCCCAGACCGCCTgtgagttcgc ... gcttctgtagTCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG