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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgaaaactagcctcaaagatttataatttctatttttctcatggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC

Basic information

species Zea mays
transcript GRMZM2G089317_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089317_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g07916.1 (Oryza sativa), 3'ss of exon 3
------------ctttgaaaactagcctcaaagatttataatttctatttttctcatggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC
            ||||  |  |||   |    |    | ||     |||  | | |||||  | ||   |    ||||||       || ||  | ||||  ||| ||| ||||||| || |||||||||||||||||| |||||||||||||||| ||||| || || ||  | |||||||| ||||| ||||||||||||||||| ||||
ataatgttccatcttttgagtctattttggttgggaaaaaa-----attgctgtgatggaa-actaaactgctggagcat------gctaaatttctttttacctttattagGTACTCGATGAGATTAGGCCATACCTTTCTGGCACAGGAGGTGGTGAGCTTGAATTCGTTGCGATCGAGGAACCTATCGTCAAGGTTAGGCTTACGGGCC
















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|148943917|gb|EC888997.2|EC888997
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|26560055|gb|CA832290.1|CA832290
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|211314413|gb|FL115082.1|FL115082
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCA-GAGAACATTGAAAAG                         GTACTTGACGAGAT
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGAT
EST: gi|78092999|gb|DV521373.1|DV521373
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|23199609|gb|BU582174.1|BU582174
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|108824268|gb|EC278276.1|EC278276
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTAGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|13557691|gb|BG549047.1|BG549047
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|6563742|gb|AW231274.1|AW231274
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|211258469|gb|FL134883.1|FL134883
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|29543551|gb|CB603933.1|CB603933
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|76290648|gb|DV030216.1|DV030216
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|18180714|gb|BM381924.1|BM381924
EST:     TTGCTGATGAGGAAACTGCCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|67017852|gb|CO446601.1|CO446601
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|45568454|gb|CK986072.1|CK986072
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|211222822|gb|FL455724.1|FL455724
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|60340325|gb|DN207298.1|DN207298
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|37377314|gb|CF625250.1|CF625250
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|71433911|gb|DR814961.1|DR814961
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|76290647|gb|DV030215.1|DV030215
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|148954266|gb|EC899670.2|EC899670
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|12973012|gb|BG268268.1|BG268268
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|148950763|gb|EC896363.2|EC896363
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|50324425|gb|CO519551.1|CO519551
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|149103365|gb|EE288750.2|EE288750
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|18178397|gb|BM379607.1|BM379607
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
EST: gi|148943916|gb|EC888996.2|EC888996
EST:     TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAG                         GTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC
genomic: TTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTC

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: 42

TGAACGGCGCTTGATGGAGAAAATACCAGAGATTGTTGCAGTTGAGCCCATTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

TGAACGGCGCTTGATGGAGAAAATACCAGAGATTGTTGCAGTTGAGCCCATTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TGAACGGCGCTTGATGGAGAAAATACCAGAGATTGTTGCAGTTGAGCCCATTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 86

TGAACGGCGCTTGATGGAGAAAATACCAGAGATTGTTGCAGTTGAGCCCATTGCTGATGAGGAAACTGGCCTTGAGTTGAACCAAGAGAACATTGAAAAGgtaaatgttc ... cctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC
                                       ttttctcctgtatc  CT-rich tract
     agtattttttaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgaaaactagcctcaaagatttataatttctatttttctcatggatcagtattttttaagagcattgagaaactgaacatgttttctcctgtatcagGTACTTGACGAGATTAGGCCATACCTTGCTGGCACAGGAGGTGGCGAGCTCGAGTTTGTCACAATCGAGGAGCCTATTGTCAAGGTTAGGCTTACAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - gaaaacta
- - - - - - - - - - - - - - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttt