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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttaccacctctaacgcagatcggttctcaaagctataaatttaacggcagtctagtcagcttgcaagagaaaattggattcagagttatccatg...

Basic information

species Zea mays
transcript GRMZM2G087192_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087192_T02 (Zea mays), 5'ss of exon 3
lower sequence: 13113.m00235 (Oryza sativa), 5'ss of exon 4
GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttaccacctctaacgcagatcggttctcaaagctataaatttaacggca-----gtctagtca---gcttgcaagagaaaattggattcagagttatccatg
|||||||| ||||| |||||||| ||||||||||| |||||    |||||||| ||||||||||||||||||||||||||||| |||||||| |||  |||||||||||| |  ||| |   |     |||| | | |||||| | ||| | |        | |||| |   ||  ||| |||||  ||  | |  || ||       
GAGCAAGTGGAAGCGTGGAAGCCAATCGTAGACGGCGTTCATGCCAAAGGAGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttactatatctgatataagcatgttcccta-gctatataattatctgtgtagacatgtagttatttgcaagcaggagaacctttaaattggattt-------

upper sequence: GRMZM2G087192_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ25413 (Selaginella moellendorffii), 5'ss of exon 3
GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttaccacctctaacgcagatcggttctcaaagctataaatttaacggcagtctagtcagcttgcaagagaaaattggattcagagttatccatg
|||||||||||||||||||||||||| ||  | |  |||||  | |||||||   | || ||    ||||||||||| || || ||||| ||  || |  ||  || |      ||| |  |     | |||   |||||  |  ||  |  ||  | |   |||                                   
GAGCAAGTCGAAGCATGGAAGCCGATTGTCCAGGCTGTTCATGACAAAGGAGCTGTTTTCTTTCTACAGATTTGGCATGTGGGAAGAGTTTCTCATACATgtgagtatg---aatctgattc---ctgattcatgaagctcgagcttacatagcgttttg--cag-----------------------------------
















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|33098560|gb|CF058520.1|CF058520
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|33098710|gb|CF058670.1|CF058670
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|91878868|gb|EB408825.1|EB408825
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|211046904|gb|FL342230.1|FL342230
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|33099068|gb|CF059028.1|CF059028
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|211434603|gb|FL306594.1|FL306594
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTATGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATTGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|211538244|gb|FL353979.1|FL353979
EST:     GGGATATTTTTSSTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: GGGATATTTTTC-TGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|32828310|gb|CD967988.1|CD967988
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         C-GTTCNAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTC-AGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTA
EST: gi|32844951|gb|CD984632.1|CD984632
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCC                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|71766717|gb|DR964654.1|DR964654
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|78110280|gb|DV528695.1|DV528695
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|13382053|gb|BG458728.1|BG458728
EST:     CACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: CACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|33099221|gb|CF059181.1|CF059181
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|71769744|gb|DR967681.1|DR967681
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|211049230|gb|FL320166.1|FL320166
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|71448418|gb|DR829468.1|DR829468
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|31363471|gb|CD447828.1|CD447828
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|32844217|gb|CD983898.1|CD983898
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|32845504|gb|CD985185.1|CD985185
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|211086396|gb|FL335516.1|FL335516
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|76017395|gb|DT944565.1|DT944565
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|71431905|gb|DR812955.1|DR812955
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|211215728|gb|FL322479.1|FL322479
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|13382062|gb|BG458737.1|BG458737
EST:     TCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: TCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|33099127|gb|CF059087.1|CF059087
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CGTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
EST: gi|76281886|gb|DV021454.1|DV021454
EST:     AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA
genomic: AGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAA

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: 64

GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAAAGCCTCAAGTGAGAGCCAATGGTATAGACGTGGCTACTTTCGCAGTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1746

GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAAAGCCTCAAGTGAGAGCCAATGGTATAGACGTGGCTACTTTCGCAGTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1796

GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAAAGCCTCAAGTGAGAGCCAATGGTATAGACGTGGCTACTTTCGCAGTTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 332

GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttac ... tccaatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCAAGCACCGATAAGCCACTAAAGCCTCAAGTGAGAGCCAATGGTATAGACGTGGCTACTTTCGCAGTTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttaccacctctaacgcagatcggttctcaaagctataaatttaacggcagtctagtcagcttgcaagagaaaattggattcagagttatccatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaaa