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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA
|||| | ||  ||||| |  ||  ||      || ||  | ||| |||   ||| |||||     ||   |||||| ||     |  ||||||||| |||||||||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||| |||||  |||||||||||||||||||||
gttaatcttcccatccaaaagtgaactg---ccaacttgtcaactttg---ttttctgaattttgttgcccattttgtt-----ccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctga-cagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA
       ||||  ||    | || ||| |   || |  |||    || | | |  || |    | |     |||  |||    | ||| |||||||| ||  | || |||||||||||||| || || || | ||||||||| ||  || ||||||||||||| || | | | ||||||||||||||||| |
------gtttg--tcttgtgataaacatagaccatc--ttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 16
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcatttt-cctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA
       ||||  ||    | || ||| |   |  ||  |  | || || |  |  |  || || || | | |  || |          |||||||| ||  |||| |||||||||||||| || || || | ||||||||| ||  || ||||||||||||| || | | | ||||||||||||||||| |
------gtttg--tcttgtgatagacatagaccgtcttgttcatctagcttaatatcctaatggattactttacattgtg-------agcagCAAGCTGAAACACAGATAAAGAGAAGAATTGGAATTGGAAACCACATATCGGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
lower sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA
     || |||| |    ||| | | | |||      || | | ||     | |  | |     |||  |    ||  | | |    ||||||||||||  |||| ||||||||||||||||| |||||    |   |||| ||| || | ||||| || |||||     | ||||| ||||| || || |
---gttagttgc-ttgtggggaagaaagaatc-----atcgtatctctagatgtaataactaaatttggta---ttggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctga-cagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA----
                   |  |  |  |  ||   | |    | || | || |     |    |   | || ||   || |   ||| |||||||| ||  |||| ||||||||||||||||| || || ||||||||||| ||| ||||||||||||||||| | | | ||||||| ||||||||||| |    
-------------gtgattgacaccctcacctccattttct--cttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT

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|67015692|gb|CO444441.1|CO444441
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|76933303|gb|DV173407.1|DV173407
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211443723|gb|FK945773.1|FK945773
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|14191099|gb|BG833329.1|BG833329
EST:     TCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: TCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|4804371|gb|AI666237.1|AI666237
EST:     CGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: CGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211443724|gb|FK945774.1|FK945774
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|5468730|gb|AI834521.1|AI834521
EST:     ATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: ATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|76933305|gb|DV173408.1|DV173408
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|78544713|gb|DV622211.1|DV622211
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211443722|gb|FK945772.1|FK945772
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211441602|gb|FK945769.1|FK945769
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|71771846|gb|DR969783.1|DR969783
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211441601|gb|FK945768.1|FK945768
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211441600|gb|FK945767.1|FK945767
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|22546223|gb|BU098534.1|BU098534
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|71435361|gb|DR816411.1|DR816411
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|211441604|gb|FK945771.1|FK945771
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAATGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|71429881|gb|DR810931.1|DR810931
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
EST: gi|149000776|gb|EE037999.2|EE037999
EST:     GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAG                         CAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCC

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: 72

AGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 19

AGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 14

AGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA


Block sizes: 40 (upstream exon), 18 (downstream exon)
Score: 2

AGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAACCTGTCACCGGAGATCGCAAACGAAATCAAGgttagtattt ... catctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA
                           ctttcatcattttttt  CT-rich tract
                            tttcatcatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT