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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG

Basic information

species Zea mays
transcript GRMZM2G399073_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 10
gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
|||||| ||| ||| |||| || | |  |    |||   || |  | | ||||     ||||| ||   ||   |||| ||| |||||| | || ||||| |||||| |||| || ||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||| || ||||||||||
gtactagattactatttcatgaacga-cacggtattccattcattgacttatgcagc-ctaaacctataagc--tattatctgtagGGTCTCGTCGACTCGGACACATTGCCTCTCAATGTATCACGAGAAATGCTCCAACAACATAGCAGCCTGAAGACCATCAAGAAGAAACTAATCCGCAAAG

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
---------gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagt-gatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
         ||  |   ||| || | ||     | ||||   || |   | | |   || | |  ||  |||| || |  | ||  ||      ||||| ||||||| || |||||  |||| || ||||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||| || ||  | ||||
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
----------gtactatattgctacttcaagagcaa-atatacaattaatttgaaaggcatatgttatactaaatcttacagt-gatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
          ||  |   ||| || | ||     || ||||   || |   | | |   || | |  || ||||| ||||  | ||  ||      ||||| ||||||| || |||||| |||| || ||||| || ||||||||||| || |||||||| ||||| ||||| ||||||||||| || ||  | ||| 
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 10
gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatct-tacagtgatattctctc-tagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
      ||   |||||| ||   ||||   |    |  ||| ||    |  |  |   |||||||  ||  ||||  | || |   ||||| |||||||||| |||||| |||| || ||||| ||| |||||||||| |||||||| |||||  | ||||| || ||||||||||| ||||| || |
-----gtaa-actacttgaaagacaaactaaggggttctttcaatacaaatttatgggctaaatccctaacgtgagttgcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTTCAACAACACAGCAGCTTAAAGACAATTAAGAAGAAGCTTATCCGAAAGG

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
--------gtactatattgctacttcaagagcaaatatacaatt---aatttgaaaggcatatgttatactaaatcttac--agtgatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
          | | |||   | | |   | |    | || | |    |||||   |   |  | |   | | | ||| |    ||||  || |    ||||| |||| || || |||||  | || || ||||| |||||||||||||| |||||||| |||||| |||| || || ||||||||||| |||||||| |
gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S8_67V6.1 (Physcomitrella patens), 3'ss of exon 11
-------gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcata-------tgttatactaaatcttacagtg------atattctctct----agGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
        | | || |  || | |  || ||      | |||| |   | |||    |       |||  | ||  | |    |         || ||   | |    ||||||||||||||||||| ||  ||||| | ||||| || ||||||||||| || ||||  |||||||| |||||  | ||||||||  |  || | ||||
gtgtgcttttcaatgtcacttcgtagagtgcttggtcaaaattgaccaggaagagtcactttgagtgtggttctggaccaaggaacacatctcatgttgcttgttgacagGGTATTGTTGACTCAGATACCTTGCCGATAAATGTCTCCCGAGAAATGCTGCAGCAACTCAGCAGTCTCAAGACCTTGAAGAAGAAAGTCGTCAGGAAAG

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|211478283|gb|FL245116.1|FL245116
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|32834169|gb|CD973847.1|CD973847
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|22489665|gb|BU049575.1|BU049575
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|31358114|gb|CD442471.1|CD442471
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTTAATGTGTCACGAGAGGGGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|19822479|gb|BQ048503.1|BQ048503
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|211478285|gb|FL245118.1|FL245118
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|211354990|gb|FL245115.1|FL245115
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC

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: 141

CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG
                                           tattctctct  CT-rich tract
                 atatgttatactaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG