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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatag

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 9
ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcacttccaattttacattgagctctg--gttggcagttagcacatgatt---aaacac-----atttctctcc-acacaatag
 ||||| |||||| ||||||||||||||||||| || || ||||| |||||||||||||| ||  ||||| | || || || |||| ||| || ||||||||| |||    |||| ||| |   | ||  ||    |  |   ||  | |||  ||    |||||     | |  ||||  |||   |||
GTCTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGGAAATTCCCAGAGAGAATTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAAGGgtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctag

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 9
ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac-----ttccaattttacattgagctc-tggttggcag--ttagcacatgattaaacacatttctctccacacaatag---
|  ||| |||||| |||||||||||||||||||||| || ||  |  | || ||| |||| ||||||||  ||||||| ||  | ||||| |||||||||||  | |        ||||    | | ||||          |  | |  ||||       |   ||| |||  | | |  |   |     
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGGgtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcag

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 9
ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcacttccaattttacattgagctctggttggcagttagcacatgattaaacacatttctctccacacaatag--------------------
    || |||||| |||||||||||||||||||||| || ||  |||| || || |||||||| || ||   |||||| ||| | ||||| |||||||| ||||| |    |   |||     |  | || | ||      | |  |  |  ||  |     ||   |     ||||                      
TAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAAGAgtatggttctcttttattcacattccaacttttgtgccttttaaatatgttgttgtaaggcctttattgtttgcaatgttccttttcaattgataccag

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|211286766|gb|FK982432.1|FK982432
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|9254689|gb|BE345157.1|BE345157
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|211286763|gb|FK982429.1|FK982429
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|87155357|gb|DY400146.1|DY400146
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|30306992|gb|CD001665.1|CD001665
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|22472855|gb|BU037335.1|BU037335
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|211132359|gb|FK982426.1|FK982426
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
EST: gi|31361304|gb|CD445661.1|CD445661
EST:     TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGG                         ATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA
genomic: TTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAA

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: 234

ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 254

ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

ATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAAGGgtatgatcac ... cacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT