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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA

Basic information

species Zea mays
transcript GRMZM5G825110_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 9
-------------------gtatacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
                   |  | | | |  | | |  ||| |  |   | | |||  |  |   |||  | |   |   | |||    |    |||||||||||| ||||||||||||||||||||||| ||||||||  |||||||||| || 
gtaagcagtgcctccttttgcttcctcgggattacttcttgaagtatggaaactgtactgtttttatttctgttgatcactctttt--gatgtggtagGATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 9
-----------------gtatacaccgcttcattgtttgcatcaataatattgtcttac-tcaaattgatata----tcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
                  | |    |   |||   | ||    ||||  ||    |||  |||  | || | |    |  | | | || | |    || |||| |||||||| || || || || |||||||||||||| || |||||||||||||| 
gtatgttctcaaaacttatgtttttctaatcaggatgtgagcaaatataatccatttaggtcaggtagaaacagacttgctgtgtgtttccatttttgcagGACTTTGGTGATAGTATTCCGGGACATGGTGGAATTACCGACAGAATGGATTGCCAG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G46440.1 (Glycine max), 3'ss of exon 9
-----------------------------------gtatacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
                                   |||  || | |    ||        |  | | | |  |  ||  |   |     |||    | ||| |||  | |  |||| ||||||||||| |||||||| ||||||||| |||| || |||||||| ||||| 
gtctgttcttgctctttatacaagacatttattttgtacccatcaccctttttccattcactttgaaactcccaaacatagcatatagcatcgatctcttt-caatgattacagGACTTTGGTGACAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
gtatacacc----gcttcattgtttgca---------tcaataatattgtcttactcaa--attgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
|||| | |      ||||  | |||| |         | |  ||   |     | | |   ||  | | |  | || | || | |    || ||||||||||||| || || || || |||||||||||||| || |||||||||||||| 
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT4G26770.1 (Arabidopsis thaliana), 3'ss of exon 8
--gtatacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaact--gtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
    | |||    |  |   ||   |    |  |||   |  |  |||    | |||| | ||  ||||       |    ||||||| || ||||||||||| || ||||| ||| ||||||| |||||||||||||||
gttaacacatttttcaaacattaaaaggttttgtatctacagatccaagaacaaatatttactagtttatgtcgctttgacagGATTTCGGAGACAGCATACCAGGACATGGAGGATTTACTGACAGAATGGATTGCCAA

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------gtatacaccgcttcattgtttgcatcaataatattgtcttact----caaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
                                  || ||   |      |  || ||  ||       || ||      ||||| | |       ||| |   ||    |  |||||||||| || || || ||||| |||||||||||||| || ||||||||||| || 
gtccacccttgttttaaacacagttgcttaaagttatactaatgtgaaatgagc-tccctatctccacctcacaacaataaattaaaaataaggatttctctgaatttttacagGATTTTGGAGATAGTATTCCTGGACATGGTGGAATTACAGACAGAATGGATTGTCAG

upper sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------gt-atacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
                              || || |     | ||| |   || ||| |  | ||| |    |    ||  |||   ||||||||   |     |  |||| ||||| || || || ||||| || |||||||||||||||||||||||||| || 
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttat---ttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG

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|32806967|gb|CD959201.1|CD959201
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|32809742|gb|CD961976.1|CD961976
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|71760475|gb|DR958412.1|DR958412
EST:     ATTCGGAGGANNNNNNNGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: ATTCGGAGGA-TTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|71426533|gb|DR807583.1|DR807583
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|78121240|gb|DV539624.1|DV539624
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|71426082|gb|DR807132.1|DR807132
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|60338336|gb|DN205309.1|DN205309
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|60344634|gb|DN211607.1|DN211607
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|76014866|gb|DT942036.1|DT942036
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|76021500|gb|DT948670.1|DT948670
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
EST: gi|76287485|gb|DV027053.1|DV027053
EST:     CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT
genomic: CATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGAT

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), 47 (downstream exon)
Score: 155

TGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCGTCAATAATAGCACCATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

TGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCGTCAATAATAGCACCATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

TGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCGTCAATAATAGCACCATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

TGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCGTCAATAATAGCACCATTCGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTCAAAATAAAGgtatacaccg ... aaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
                    aaattgatatatcttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA