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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacggataggcaaattccatctaaccctttctccttggtctgtggtgctaaagattgaatttgcag

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g10180.2 (Oryza sativa), 5'ss of exon 4
ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgat-------------------acggataggcaaa--ttccatctaaccctttctccttggtctgtggtgctaaagattgaatttgcag
|||| | |||||||||||||| || || |||   ||||||||||||||| |||| |||||||||||||||||||| |||||||||||||  ||||||||||| |  |                   | ||| ||  |||  || |||||||   | ||||  |   |||  || ||||| || || ||| |||
ATTAGAGTCTGCTTATGGCCAGTTTGAGTCTCATGACTTCTCAAAAGTCCTGGATTACATCAACAAAATTGTGCTTGTTTTTTCTCCAGACTGCTTAAAGgtatatttcagaggatagtaggaaccatggacagataaatatttcatctaattttgtctcagtaagctgcagtactaaaaatggatttttcag

upper sequence: GRMZM2G341404_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g74580.1 (Oryza sativa), 5'ss of exon 3
ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgat-------------------acggataggcaaa--ttccatctaaccctttctccttggtctgtggtgctaaagattgaatttgcag
|||| | ||||||||||||||||| || |||   ||||||||||||||| |||| |||||||||||||||||||| ||||||||||||   ||||||||||| |  |                   | ||| ||  |||  || |||||||   | ||||  |   |||  || ||||||||||| ||| |||
ATTAGAGTCTGCTTATGGCCAATTTGAATCTCATGACTTCTCAAAAGTCCTGGAGTACATCAACAAAATTGTGCTTGTTTTTTCTCCAAACTGCTTAAAGgtatatttcagaggatagtaggaatcatggacagctaaatatttcatctaattttgtctcagtaagctgcagtactaaagattgatttttcag
















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|148940996|gb|EC885847.2|EC885847
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|149079408|gb|EE168385.2|EE168385
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|148970832|gb|EE021601.2|EE021601
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|78080724|gb|DV509136.1|DV509136
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|71323581|gb|DR798459.1|DR798459
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|87155508|gb|DY400297.1|DY400297
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|78104565|gb|DV522983.1|DV522983
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|211247228|gb|FL156668.1|FL156668
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|91875154|gb|EB405111.1|EB405111
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|149010182|gb|EE041997.2|EE041997
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|148960799|gb|EE011462.2|EE011462
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|211245008|gb|FL156664.1|FL156664
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTNGAA-GACTACTNCA-
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACT-GAAAGACTACT-CAA
EST: gi|26558848|gb|CA831083.1|CA831083
EST:     CGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|101391578|gb|EB817725.1|EB817725
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTNAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACT
EST: gi|67016841|gb|CO445590.1|CO445590
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|22546040|gb|BU098361.1|BU098361
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
EST: gi|148940390|gb|EC885183.2|EC885183
EST:     TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAG                         GCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT
genomic: TGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGT

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), 49 (downstream exon)
Score: 70

ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGTGTTATTTCAGAGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59

ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGTGTTATTTCAGAGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67

ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGTGTTATTTCAGAGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 200

ATTACAATCTGCTTATGGCCAATTCGATTCTGGAGACTTCTCAAAAGTCGTGGAATACATCAACAAAATTGTGCTGGTTTTTTCTCCAGGTTGCTTAAAGgtgtgatacg ... gaatttgcagGCAAAGCTTCTCAAGGCTAAAGCATTGCTAGCACTGAAAGACTACTCAAGTGTTATTTCAGAGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGG