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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtaattattgcctcttgtattctattatagaaacacaaaacttggaagaacttctaggaagtccacaaaatagcctctgaacctgttgtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT

Basic information

species Zea mays
transcript GRMZM2G071071_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071071_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 11
-------acagtaattattgcctcttgtattctattataga----aacacaaaacttggaagaacttctaggaagtccacaaaatagcctctgaacctgttgtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT
       |||| |||  |||| |||||| | |   ||||       |  ||||   |  |  |  ||||     || ||| ||||      |   ||||||  | ||||||||||||||||| ||| ||||||||| | || || ||||||||| ||||||||||||||||||||||||||||||| |||||||| ||  |||| ||||||
acacacaacagcaat-gttgc-tcttgtttccggatatatctttttatgcaaattgtatataattttct-----gtacactaaatg----ttatgcctgtttaaatggcagCTGTGATGAATTTTCTTGGCAAAGAACAAGGGATTTGCTTGTGGAAGTGGCTACACATGGAGAAAATACTGGCTATGAAGTTCCTTGTCTGATTGTTGCT

upper sequence: GRMZM2G071071_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 3'ss of exon 12
aca-gtaattattgcctcttgtattctattatagaaacacaaaacttggaagaacttctaggaagtccacaaaatagcctctgaacctgttgtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT
|||  ||| |||||  | ||    | ||   |      | |  |  |         |     |  | |   | | |   | |||  |||||| | ||||||  ||||||||  ||| ||||||||||| ||||| |||||||| |||||||| ||||  ||| |||| |||||||| |||||||| ||  |||||||||||
acacataaatattgtttattcagatgtacc-tctctctatattatctattcagttgtacctaattttctgcacacaaaatgtgatgctgttgaaatggcagTGGTGATGAAGTTTCTTGGCAAAGAGCAAGAGAATTGCTTGTACAAGTGGCCACACGGGGAAAAAACACTGGCTATGAAGTTCCTTGTCTGATAGTTGCT
















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|31359528|gb|CD443885.1|CD443885
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|67019644|gb|CO448393.1|CO448393
EST:     GACAGGGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32841088|gb|CD980769.1|CD980769
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|67017730|gb|CO446479.1|CO446479
EST:     GACAGGGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32840501|gb|CD980182.1|CD980182
EST:     AGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: AGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|60345129|gb|DN212102.1|DN212102
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32840298|gb|CD979979.1|CD979979
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|31356495|gb|CD440852.1|CD440852
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|31357304|gb|CD441661.1|CD441661
EST:     CCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: CCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32840287|gb|CD979968.1|CD979968
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32839739|gb|CD979420.1|CD979420
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|87152121|gb|DY396910.1|DY396910
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32839495|gb|CD979176.1|CD979176
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGGGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|18385253|gb|BM418452.1|BM418452
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32839754|gb|CD979435.1|CD979435
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32933393|gb|CF038205.1|CF038205
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
EST: gi|32840274|gb|CD979955.1|CD979955
EST:     GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAG                         CTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC
genomic: GACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 321

CACTAATATTGCGAGAGATTCCTGAAGGTGATGTGAGATCGATACTTTCTGACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 241

CACTAATATTGCGAGAGATTCCTGAAGGTGATGTGAGATCGATACTTTCTGACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 224

CACTAATATTGCGAGAGATTCCTGAAGGTGATGTGAGATCGATACTTTCTGACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 333

CACTAATATTGCGAGAGATTCCTGAAGGTGATGTGAGATCGATACTTTCTGACAGAGAATCATTGGCGCCGTGTGATGTAGCAGTATTTGTTTACGATAGgtgcacactg ... gtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaagaacttctaggaagtccacaaaatagcctctgaacctgttgtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT
                      acaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtaattattgcctcttgtattctattatagaaacacaaaacttggaagaacttctaggaagtccacaaaatagcctctgaacctgttgtattggcagCTGTGATGAATATTCATGGCAAAGAGCTAGAGACTTGCTTGTGCAAGTGGCTACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - cttgtat
- - - - - - - - - - - - - - - - -aaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaacc