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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agccatcctttaaaagtcatgaaaacggatatgtttgccgcgatattgctctccaatggtggctgtattggatgtttttctgatgactgcggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG

Basic information

species Zea mays
transcript GRMZM2G161337_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g15780.4 (Oryza sativa), 3'ss of exon 8
agccatcctttaaaagtcatgaaaacgga--tatgtttgccgcgatattgctctccaatggtggctgtattggatgtttttctgatgactgcg----gcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG
 |      ||      |   ||   | ||   ||| ||||    || |  |       |   |  ||| ||      |||||| |||| | |      ||||  |||| |||||||| ||||| |||||||||||||| || |||||||||||  | ||||||||||| ||||||||||| || |||
-gtttgtgttcttttttttcgatggctgagtcatggttgcattaatttgacagatttgttaggaatgtgttaacaacttttcttatgattactttctacttggcagGTCTCCAAACCTGGATCTGTGAAGGTGGAGAAATTAATGAACATTGAACGCTACTCCCATGTCATGCACATCAGTTCCACG

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G23680.2 (Glycine max), 3'ss of exon 8
---agccatcctttaaaagtcatgaaaacggatatgtttgccgcgatattgctctccaatggtggctgtattggatgtttttctgatg-actgcggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG-------------------
    |   |   | |  |  | |         | ||  ||| ||  ||   |  | |  |  ||    | || |   | |   | ||| |    |  |    |||| |||||||| || || ||  | || || ||| | ||||| |||||| | || ||||||||||||||||||||||||||                    
ttgggtagtttatgatcacactttttctaaattgtgcatgctgctgtaaaccgtttcttttatg----ttttagccatgtgcttaatgcaagatgaatatgcagGTCTCCAAACCGGGTTCTGTTCAAGTTGAAAAGCTTATGAATATTGAGCGCTATTCCCATGTTATGCACATCAGCTCAACAGTAAGTTCCTTTAGCAAAA

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G23680.1 (Glycine max), 3'ss of exon 8
---agccatcctttaaaagtcatgaaaacggatatgtttgccgcgatattgctctccaatggtggctgtattggatgtttttctgatg-actgcggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG
    |   |   | |  |  | |         | ||  ||| ||  ||   |  | |  |  ||    | || |   | |   | ||| |    |  |    |||| |||||||| || || ||  | || || ||| | ||||| |||||| | || |||||||||||||||||||||||||| 
ttgggtagtttatgatcacactttttctaaattgtgcatgctgctgtaaaccgtttcttttatg----ttttagccatgtgcttaatgcaagatgaatatgcagGTCTCCAAACCGGGTTCTGTTCAAGTTGAAAAGCTTATGAATATTGAGCGCTATTCCCATGTTATGCACATCAGCTCAACA

upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 3'ss of exon 8
agccatcctttaaaagtc-atgaaaacggatatgt-ttgccgcgatattgctctccaatggtggctgtattgg--atgtttttctgatgactgcggcttg-----atagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG
         ||| | ||| ||  | |   ||||   ||| |   || |   | ||  |   |     || |||  ||  |||| |  | | | |    ||     | |||| |||||||| || || ||||  || || ||| | ||||| |||||| | ||||||||||| |||||||||||||| |||
---------ttatatgtctatatatatatatataaattgtctaaatttctttttcagagcatatgcttaatggccataattttgtagttaatactagctgttcttacagGTGTCCAAACCTGGTTCTGTGACTGTTGAAAAGCTCATGAATATTGAGCGCTACTCCCATGTCATGCACATCAGCTCCACG

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|13178323|gb|BG349581.1|BG349581
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|71429501|gb|DR810551.1|DR810551
EST:     GTGCCGAGCACATAATGCTTGTGGACTGGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|33099478|gb|CF059438.1|CF059438
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|71761802|gb|DR959739.1|DR959739
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|71762476|gb|DR960413.1|DR960413
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|67014966|gb|CO443715.1|CO443715
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|71314990|gb|DR794114.1|DR794114
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|31364516|gb|CD448871.1|CD448871
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|116816802|gb|EC859574.1|EC859574
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGAGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|33093179|gb|CF053173.1|CF053173
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|71448131|gb|DR829181.1|DR829181
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|60357763|gb|DN224736.1|DN224736
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|32836831|gb|CD976509.1|CD976509
EST:     TG-CGANGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAACCCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: TGCCGA-GCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|7238168|gb|AW573390.1|AW573390
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|32866600|gb|CF006282.1|CF006282
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|13178556|gb|BG349814.1|BG349814
EST:     AAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: AAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|60398523|gb|DN231339.1|DN231339
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|211345792|gb|FL266265.1|FL266265
EST:     AGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: AGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|60344440|gb|DN211413.1|DN211413
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|211345789|gb|FL266262.1|FL266262
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|211345791|gb|FL266264.1|FL266264
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|32836931|gb|CD976609.1|CD976609
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|67024314|gb|CO453063.1|CO453063
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|211282582|gb|FL175928.1|FL175928
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
EST: gi|149026791|gb|EE046153.2|EE046153
EST:     GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAG                         GTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA
genomic: GTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGA

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), 32 (downstream exon)
Score: 21

GAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAACAGTGTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

GAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAACAGTGTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

GAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAACAGTGTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 21

GAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAACAGTGTGCCGAGCACATAATGCTTGTGGACTTGGGAAGGAATGATGTTGGCAAGgtctgtattt ... ggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctctccaatggtggctgtattggatgtttttctgatgactgcggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG
                                ttctgat  putative branch site (score: 21)
                          atgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agccatcctttaaaagtcatgaaaacggatatgtttgccgcgatattgctctccaatggtggctgtattggatgtttttctgatgactgcggcttgatagGTATCCAAACCAGGATCAGTGAAGGTGGAGAAGTTGATGAACATTGAGAGATACTCCCATGTTATGCACATCAGCTCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
-gccatcc
- - - - - - - - -catgaaa
- - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc