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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagggattctattttctgatagttctcttctttgattaatgctgccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA

Basic information

species Zea mays
transcript GRMZM2G179429_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 4
gttagggattctattttctgatagttctcttctttgattaatgctgccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA
|||  |||  | | ||    |  | ||     | || || ||  ||| ||    |||| |  | ||  |||  | |  || | || |   |||||||||||||| |||||  | ||||| || |||||||  |||||||| || || ||||||||||||||||| |||||||| |||||||||||||||||||
gtt--ggacaccactt---aactgctcatcattctgtttgatattgctat----tcagctccagtt--gacttgattgtttaattgttt-tagGAAGAAGAAGCAAGGGCGAGGAAAGCCAAAGAGGAGGAAGCTGCTGCCTTGGAATTTGAGAAATGGAAAGGAGCCTTCTCAGTTGATGCTGAAGGTACAA

upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G36410.1 (Glycine max), 3'ss of exon 4
gttagggattctattttctgatagttctcttctttgattaatgct---gccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA
  |  |  |  ||  || |     ||   || | |||||||   |   |   | | || | |  |||  |  ||  |||  |||||| ||  ||||||||| ||||| || || |  || || ||||||||||  |||||||| |||||||||||||| |||||||| |  || || ||||||| ||| |||||  
-gtgagcttgttaccttgttccgatttgattttatgattaacattcatgtggtatattaactggtaaggc--acttgctt-ttaattcat--atagGAAGAGGAAGCCAGAGCTCAGAAGGCTAAGGAGGAGGAGGCTGCTGCATTAGAGTTTGAGAAGTGGAAAGGTGAATTTTCAGTTGATGATGAGGGTACCC

upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G34150.1 (Glycine max), 3'ss of exon 4
gttagggattctattttctgatagttctcttctttgattaatgctgccatgttttcagttataattctgac--aagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA
  |  |  |  ||  || |     ||   || |  |||||    |   ||| ||| | | |      || |  | |||  | |   |    ||||||||| ||||| || || |  || || ||||||||||  |||||||| |||||||||||||| |||||||| |  || || ||||||| |||||||||  
-gtgagtttgttacctttttccgatttgattttaggattagcattcttatggttt-attaactggcatggcccatgcttttcatgattcatatagGAAGAGGAAGCCAGAGCTCAGAAGGCTAAGGAGGAGGAGGCTGCTGCATTAGAGTTTGAGAAGTGGAAAGGTGAATTTTCAGTTGATGATGAAGGTACCC

upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G27120.2 (Arabidopsis thaliana), 3'ss of exon 5
gttagggattctattttctgatagttctcttctttgattaatgctgccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA
    |    || ||  ||| | | |||  ||  ||   || |  | |    |||  | |  |     || | |  |     |||  | | |||||||||||||  |  || ||| |||| || || || |  || ||||| ||||||||||| |||||||||||||  || || ||||||||||||||||| |
----gtaggtcaatcatctcagatttcgttttgtta--tagtcttcctgcttttgaaatactgggcttggctaattgtgacattgttacgtagGAAGAAGAAGAAAAAGCGCGACAAGCCAAAGAAGAAGAGGCAGCTGCGTTAGAGTTTGACAAATGGAAAGGGGAATTTTCAGTTGATGCTGAAGGTACTA

upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0177g00150.t01 (Vitis vinifera), 3'ss of exon 4
gttagggattctattttctgatagttctcttctttgattaatgctgccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA
    | || | | | ||||     ||   ||  | | | |    |    | | ||  |||    | || | ||  | |  |   | |    |||||||||||||||  || | ||| || |||||||| |  || ||||| || ||||||||||| |||||||| |  || ||||||||||| ||||||||||
----gtgagtttgtcttct-----ttgcttttctggttcaggaatatactttcttgtgttcccttcctaagaatttcaacatggtttattcagGAAGAAGAAGCTAAAGCTCAAAAGGCCAAGGAGGATGAAGCAGCTGCATTGGAGTTTGAGAAGTGGAAAGGAGAATTTTCTGTTGATGCAGAAGGTACAA

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|31364620|gb|CD448975.1|CD448975
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCGCGGAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|71757661|gb|DR955598.1|DR955598
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|50329493|gb|CO524619.1|CO524619
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|89248029|gb|DY619815.1|DY619815
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|71773570|gb|DR971468.1|DR971468
EST:     AATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCAC-AGAAGAGGC-ATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAG-AGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|94472565|gb|EB701523.1|EB701523
EST:     AGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGTTAGGGCACGAAAAAGCAAAGGAGGAGGCTGCTGCTGCTTT
genomic: AGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACG-AAAAGCAAAGGAGGAGGCTGCTGCTGCTTT
EST: gi|91057069|gb|EB167487.1|EB167487
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|91048409|gb|EB158827.1|EB158827
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|76014913|gb|DT942083.1|DT942083
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|78112542|gb|DV530936.1|DV530936
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|18384245|gb|BM417444.1|BM417444
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCGCGGAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|148958245|gb|EC904458.2|EC904458
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|71307153|gb|DR789747.1|DR789747
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|71773571|gb|DR971469.1|DR971469
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|31364129|gb|CD448484.1|CD448484
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCGCGGAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|60357983|gb|DN224956.1|DN224956
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|87153892|gb|DY398681.1|DY398681
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCGCGGAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|148956262|gb|EC902060.2|EC902060
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|148959747|gb|EC905644.2|EC905644
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|148932548|gb|EC876363.2|EC876363
EST:     AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         GAAGAAGAAGCTAGGGCGCGGAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
EST: gi|78112541|gb|DV530935.1|DV530935
EST:     AATGAGGA-GAAGAAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTG                         AAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA
genomic: AATGAGGAGGAAG-AAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 120

CGAAGAACCTGCACGGGATTCATGGAGGAGTAAACAAGACCGATACGACGAAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 178

CGAAGAACCTGCACGGGATTCATGGAGGAGTAAACAAGACCGATACGACGAAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 170

CGAAGAACCTGCACGGGATTCATGGAGGAGTAAACAAGACCGATACGACGAAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

CGAAGAACCTGCACGGGATTCATGGAGGAGTAAACAAGACCGATACGACGAAATGAGGAGGAAGAAGGATGAGGAGCGTGAGGCACAAGAGAGGCAATTGgttagggatt ... ttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgctgccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA
                                            tttatcc  CT-rich tract
                                     taattaatttatccat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagggattctattttctgatagttctcttctttgattaatgctgccatgttttcagttataattctgacaagctaattaatttatccatagGAAGAAGAAGCTAGGGCACGAAAAGCAAAGGAGGAGGCTGCTGCTGCTTTAGAGTTTGAGAAATGGAAAGGGGCCTTCTCTGTTGATGCTGAAGGTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG