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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccctcataaacaattcattgaaattatatttgttctggtaccaactacagttgttttgattatgtag

Basic information

species Zea mays
transcript GRMZM2G131756_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131756_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os05g37410.1 (Oryza sativa), 5'ss of exon 19
AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtc-----tccctcata-aacaattcattgaaattatatttgttctggtaccaactacagttgttttgattatgtag
|| ||||||||||| || ||  || |   |||||||  | ||||||||||||| ||||| ||||| |  || ||||||||||| || ||||||||||||||||  |     || | |||| ||  | |||  |||||  ||| |||     |||| || || ||| |||| ||| | |||
AGTTCTAGCCACAATCCCATAAATATCCCAAGGGAGCAGTTATGGAACTTGCATAGGCGTATGGTTTACTTTGGGACTTCAGTGCCAACCATATTCAAAGgttaccaccattcacccatacaatgactca--gaaatcttatctgtaacattaccgacaactgttatttttattctttag

upper sequence: GRMZM2G131756_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os05g37350.1 (Oryza sativa), 5'ss of exon 18
AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtc-----tccctcata-aacaattcattgaaattatatttgttctggtaccaactacagttgttttgattatgtag
|| ||||||||||| || ||  || |   |||||||  | ||||||||||||| ||||| ||||| |  || ||||||||||| || ||||||||||||||||  |     || | |||| ||  | |||  |||||  ||| ||      |||| || || ||| |||| ||| | |||
AGTTCTAGCCACAATCCCATAAATATCCCAAGGGAGCAGTTATGGAACTTGCATAGGCGTATGGTTTACTTTGGGACTTCAGTGCCAACCATATTCAAAGgttaccaccattcacccatacaatgactcaaagaaatcttatctgcaactttaccgacaactgttattttcattctttag
















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|32913514|gb|CF018326.1|CF018326
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|211540330|gb|FL320588.1|FL320588
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTTAGAACAGAAGAAATACAANCA-TGCTTCTGGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAA-CAATGCTTCTGG-AGGG
EST: gi|211151599|gb|FL276380.1|FL276380
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|60339031|gb|DN206004.1|DN206004
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|60358415|gb|DN225388.1|DN225388
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|60347567|gb|DN214540.1|DN214540
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|31364194|gb|CD448549.1|CD448549
EST:     CATATTCAAAG                         GTCTAAGAACAGAAGAAATACACCAATGCTTCTGGAGGG
genomic: CATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|211181361|gb|FL452266.1|FL452266
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAMCAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|60394289|gb|DN227159.1|DN227159
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|211151600|gb|FL276381.1|FL276381
EST:     TTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: TTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|9731007|gb|BE509759.1|BE509759
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|5901234|gb|AW042334.1|AW042334
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|211428318|gb|FL475012.1|FL475012
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAG                         GTTTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
EST: gi|60353813|gb|DN220786.1|DN220786
EST:     GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAA-                         GTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG
genomic: GCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG

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), 49 (downstream exon)
Score: 226

AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 30

AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 41

AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccc ... gattatgtagGTCTAAGAACAGAAGAAATACAACAATGCTTCTGGAGGG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTACCCACCATATTCAAAGgttgtctccctcataaacaattcattgaaattatatttgttctggtaccaactacagttgttttgattatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG