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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccttctttttcccgtctctgctctcacctcggtttcggtttggtttcttgcgtggctgtttccaatgattaatctcatctggcggctgccccgtggtttgggttgggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG

Basic information

species Zea mays
transcript GRMZM2G461793_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g17040.1 (Oryza sativa), 3'ss of exon 1
gtagccttctttttcccgtctctgctctcacctcggtttcggtttggtttcttgcgtggctgtttccaatgattaatctcatctggcggctgccccgtggtttgggttgggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG
                  | | |||   ||   | |      | |  |||||| |||      |     || |   |    |||| ||         |||||| ||||  || |  ||||||||| |||||||| ||||| || ||||| |||||||| || || || |||||||||||||||||||| ||||||||||||||||| ||||||||||| 
---------------gtatatatgcgagcagagcagcaatcatcttctttctttcgttcgctgtggtggtgttctttgatttctgacgataa----atggttttggttttgcgg--cagGATCACGACGGGGATATTCTGCCGGAACCCGTACAACGCCACCGGAATATGCAACCGGAGCTCCTGCCCTCTTGCCAACAGCCGCTACGCCACCATCCGC

upper sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 1
gtagccttctttttcccgtctctgctctcacctcggtttcggtttggtttcttgcgtggctgtttccaatgattaatctcatctggcggctgccccgtggtttgggttgggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG
                 ||   |   |   |  |  |      ||  |||||  ||| |||||      || |   |    |||| ||         |||||| ||||  || |  ||||||||| |||||||| ||||| || ||||| |||||||| || || || |||||||||||||||||||| || |||||||||||||| ||||||||||||
-----------------gtacgtatgcgagcagcaatcctatcttc-tttctctcgtcgctgt----ggtgttctttgatttctgacgataaat---tggttttggttttgcgg--cagGATCACGACGGGGATATTCTGCCGGAACCCGTACAACGCCACCGGAATATGCAACCGGAGCTCCTGCCCTCTCGCCAACAGCCGCTACGCCACCATCCGG
















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|149079012|gb|EE167880.2|EE167880
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATTCT
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCAT-CT
EST: gi|93012902|gb|EB638422.1|EB638422
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|71330256|gb|DR801876.1|DR801876
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|148939429|gb|EC883983.2|EC883983
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211291475|gb|FL225666.1|FL225666
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211345141|gb|FL350534.1|FL350534
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211248875|gb|FL353267.1|FL353267
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|31355775|gb|CD440132.1|CD440132
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211008090|gb|FL365103.1|FL365103
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|76932105|gb|DV172945.1|DV172945
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211373401|gb|FL472199.1|FL472199
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|29130836|gb|CB381540.1|CB381540
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|148946083|gb|EC891379.2|EC891379
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211286714|gb|FL323329.1|FL323329
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|91872818|gb|EB402775.1|EB402775
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211526412|gb|FL361960.1|FL361960
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|148987550|gb|EE031415.2|EE031415
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|33467372|gb|CF244421.1|CF244421
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|71431373|gb|DR812423.1|DR812423
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|94477914|gb|EB706872.1|EB706872
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|211360103|gb|FL362300.1|FL362300
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|71322072|gb|DR797726.1|DR797726
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|31355774|gb|CD440131.1|CD440131
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
EST: gi|148953458|gb|EE152961.2|EE152961
EST:     GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAA                         GATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG
genomic: GACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 255

TTAAGCAGGGGAGGAGCCGGCCCTGAGCGGCGGAGTCCAAAATGAGTGACGACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 191

TTAAGCAGGGGAGGAGCCGGCCCTGAGCGGCGGAGTCCAAAATGAGTGACGACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 301

TTAAGCAGGGGAGGAGCCGGCCCTGAGCGGCGGAGTCCAAAATGAGTGACGACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 197

TTAAGCAGGGGAGGAGCCGGCCCTGAGCGGCGGAGTCCAAAATGAGTGACGACGTGGTATGGCACTGCATCCGCCACAACCACTGCAGCTTCATGTCCAAgtagccttct ... ggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaatgattaatctcatctggcggctgccccgtggtttgggttgggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG
      gattaat  putative branch site (score: 197)
     tgattaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagccttctttttcccgtctctgctctcacctcggtttcggtttggtttcttgcgtggctgtttccaatgattaatctcatctggcggctgccccgtggtttgggttgggctgtgcagGATCACAACGGGGATCTTCTGTCGCAACCCCTACAACGCGACGGGCATCTGCAACCGGAGCTCCTGCCCGCTTGCCAACAGCCGCTATGCCACCATCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT