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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaccctgttctttacacttaaactgcttctgttggaaaatctctcatgttatttcttttgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC

Basic information

species Zea mays
transcript GRMZM2G475867_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 17
gtgcaccctgttctttacac------ttaaactgcttctgttggaaaatctctcatgt-tatttcttttgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC
|| ||   ||   || ||         || |  | |||| || |||||| | |||| | ||  |||||  ||   ||||||||||| |||||| || || ||||||||||| ||||| ||||| ||||| |||  ||||||||||||||||||||||||||||||||||||||| || 
gtacattgtgaagttaacttaaaaggctatagagtttctattagaaaatatgtcatctgtaaatctttctttgtgcagTAACTCAATGAAAGAGCTCAGCCCACATATTGCCTCTGTCATGAATATTCTGGAGAACCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAGCTG
















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|32924251|gb|CF029063.1|CF029063
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924522|gb|CF029334.1|CF029334
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924638|gb|CF029450.1|CF029450
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924314|gb|CF029126.1|CF029126
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32848274|gb|CD987955.1|CD987955
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924177|gb|CF028989.1|CF028989
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924022|gb|CF028834.1|CF028834
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924179|gb|CF028991.1|CF028991
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGACCATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924558|gb|CF029370.1|CF029370
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32923896|gb|CF028708.1|CF028708
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32923795|gb|CF028607.1|CF028607
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGTAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924605|gb|CF029417.1|CF029417
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGTCT-CTGTTATGAACATTC
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTG-CTTCTGTTATGAACATTC
EST: gi|32924330|gb|CF029142.1|CF029142
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32923682|gb|CF028494.1|CF028494
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924338|gb|CF029150.1|CF029150
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|9952966|gb|BE639549.1|BE639549
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924097|gb|CF028909.1|CF028909
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32923641|gb|CF028453.1|CF028453
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924376|gb|CF029188.1|CF029188
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924146|gb|CF028958.1|CF028958
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGGCT-CTGTTATGAACATTC
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTG-CTTCTGTTATGAACATTC
EST: gi|32923916|gb|CF028728.1|CF028728
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32923936|gb|CF028748.1|CF028748
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|56462016|gb|CK986314.1|CK986314
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32923696|gb|CF028508.1|CF028508
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT
EST: gi|32924087|gb|CF028899.1|CF028899
EST:     TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAG                         TAACTCAATGAAAGAACTTAGTCCACATATTGCCTCTGTTATGAACATTCT
genomic: TATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCT

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), 46 (downstream exon)
Score: 66

TTGAGAATGCCACTTCAGACTCTGAGAAGCTATCTCCAAGATTTCTAGGCTATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 70

TTGAGAATGCCACTTCAGACTCTGAGAAGCTATCTCCAAGATTTCTAGGCTATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 41

TTGAGAATGCCACTTCAGACTCTGAGAAGCTATCTCCAAGATTTCTAGGCTATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 49

TTGAGAATGCCACTTCAGACTCTGAGAAGCTATCTCCAAGATTTCTAGGCTATTTTCTGTTCCGTTCACCTTATAAGCGGCAATCTTCTGATTTGAAAAGgtgcaccctg ... tgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacttaaactgcttctgttggaaaatctctcatgttatttcttttgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC
                                   ttatttcttttgttc  CT-rich tract
                                atgttatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaccctgttctttacacttaaactgcttctgttggaaaatctctcatgttatttcttttgttcgacagTAACTCAACGAAAGAACTTAGTCCACATATTGCTTCTGTTATGAACATTCTAGAGCGCCATGCTAGCTATTTGATGTCTGGCAAGGAGCTTTCTAAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT