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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatcttgcctttcctttgcttttgatctatctgtgtttgtttgtgttatattggctaaattataggaaggttggttgaaagcgtagcaggtgcac...

Basic information

species Zea mays
transcript GRMZM2G113470_T01
intron # 2
splice site 5'
intron type U2

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|32796742|gb|CD948978.1|CD948978
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|211350454|gb|FL030225.1|FL030225
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32787717|gb|CD936619.1|CD936619
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|9961456|gb|BE644439.1|BE644439
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32789470|gb|CD941706.1|CD941706
EST:     TCATCCTCGCAGGCGCAGAGTACACGGNGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|32799406|gb|CD951642.1|CD951642
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|15208907|gb|BI430791.1|BI430791
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350458|gb|FL030229.1|FL030229
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|8576937|gb|BE129574.1|BE129574
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32796050|gb|CD948286.1|CD948286
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|32806579|gb|CD958813.1|CD958813
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCAGGGCGTATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|4827620|gb|AI668312.1|AI668312
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350457|gb|FL030228.1|FL030228
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|78025445|gb|DV493832.1|DV493832
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|149100062|gb|EE186113.2|EE186113
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350456|gb|FL030227.1|FL030227
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32797913|gb|CD950149.1|CD950149
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|149100063|gb|EE186114.2|EE186114
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|32801538|gb|CD953774.1|CD953774
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGC
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGC
EST: gi|32789714|gb|CD941950.1|CD941950
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTA
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTA
EST: gi|60353657|gb|DN220630.1|DN220630
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGATAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|78179554|gb|DV549927.1|DV549927
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCGTATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|211350455|gb|FL030226.1|FL030226
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
EST: gi|14701476|gb|BI233894.1|BI233894
EST:     TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAAT                         GCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG
genomic: TCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTG

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: 49 (upstream exon), 48 (downstream exon)
Score: 28

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 36

CCGCAACGTCATCCTCAAGACCTTGCTGCTCTCAACCTCCATCGTCTCCGTCATCCTCGCAGGCGCAGAGTACACGGGGCCGTCTATGAACCCAGCTAATgtcagtatct ... tcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA