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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttctttctgttatagtgttatttcccttttgttttaatggcttgctatcccatcaaattaatctcatcagtctaatacttcaagtttgtgatcag

Basic information

species Zea mays
transcript GRMZM2G031824_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031824_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g22440.1 (Oryza sativa), 5'ss of exon 2
TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttctttctgttatagtgttatttcccttttgttttaatggcttgctatcccatcaaattaatctcatcagtctaatacttcaagtttgtgatcag
 ||||||||||||||||||||||||||||| || |||||||||||||| || |||||||||||||||||||||||||| |||||||||||| || ||||||||||||||||| |    | ||| || |||||||  | |||| |        ||||  ||||||||||||| |    |  |||  |||  ||||||||||||
GTTTGCAACACCATATAGGATAACATGGGATTACTATTTTGCTGCTCGAGAACACACTTTGGAGATTAAATCATGGGAAGAAGAAGCGGAACTGGAATATgtgtgttttcttccc---aaagt-ttctttccctcctttttttaccatgcaatatcttatcaaattaatcttaatgatacaatctttcgtgtttgtgatcag

upper sequence: GRMZM2G031824_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G04400.1 (Glycine max), 5'ss of exon 2
TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttctttctgttatagtgttatttcccttttgttttaatggcttgctatcccatcaaattaatctcatcagtctaatacttcaagtttgtgatcag
|||||||||||| |||||||| ||||||||||| |||||  |||| || || || |||||| || || | |||||||| ||    || || ||| ||||||| | ||| | || | || |  | |  ||||  || |||||||||   ||  ||         |  ||  ||  ||   ||||| |   | |   | |||||
TTTTGCAACACCTTATAGGATTACATGGGACTACTATTTCTCTGCGCGAGAACATACTTTGCAGTTTGATTCATGGGAAGAGCCTGCAGAGTTGGAATATgtat-tttcccttttctttttttttgttttctattctgttttaatt-ttttttaatgtggagtagcaacttcggcaaggtaatattcttaataaattatcag
















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|149104788|gb|EE290251.2|EE290251
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|71775022|gb|DR972900.1|DR972900
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|149007773|gb|EE040269.2|EE040269
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|78111913|gb|DV530309.1|DV530309
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|71430819|gb|DR811869.1|DR811869
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|32839581|gb|CD979262.1|CD979262
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|148973114|gb|EE024181.2|EE024181
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|149100419|gb|EE186494.2|EE186494
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|148940292|gb|EC885074.2|EC885074
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|78076415|gb|DV504849.1|DV504849
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|149078582|gb|EE167366.2|EE167366
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGTATTTCTATTTTTCTCATGCCATCTGGAATGC
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGC
EST: gi|211056025|gb|FL008161.1|FL008161
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|32842171|gb|CD981852.1|CD981852
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|211056020|gb|FL008156.1|FL008156
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|78075988|gb|DV504422.1|DV504422
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|148996938|gb|EE035750.2|EE035750
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|78121398|gb|DV539782.1|DV539782
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|91875426|gb|EB405383.1|EB405383
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|211056027|gb|FL008163.1|FL008163
EST:     AGCACACTTTGGAGATTAA-TCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|32840051|gb|CD979732.1|CD979732
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|78113167|gb|DV531561.1|DV531561
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
EST: gi|211471361|gb|FL048951.1|FL048951
EST:     AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATAT                         GTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA
genomic: AGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGA

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: 252

TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGAACTTTGCTATCTTTGATTGATGTCCTGCCTTTGTTTTCAAACACTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 513

TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGAACTTTGCTATCTTTGATTGATGTCCTGCCTTTGTTTTCAAACACTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGAACTTTGCTATCTTTGATTGATGTCCTGCCTTTGTTTTCAAACACTGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 734

TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttc ... ttgtgatcagGTGAAGGAGCATGGCATTTCTATTTTTCTCATGCCATCTGGAATGCTCGGAACTTTGCTATCTTTGATTGATGTCCTGCCTTTGTTTTCAAACACTGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGCAACACCATATAGGATAACATGGGACTATTATTTTGCTGCTCGGGAGCACACTTTGGAGATTAAATCATGGGAGGAAGAAGCGGAATTGAAATATgtgtgttttctttctgttatagtgttatttcccttttgttttaatggcttgctatcccatcaaattaatctcatcagtctaatacttcaagtttgtgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC