Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT

Basic information

species Zea mays
transcript GRMZM2G132968_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 4
--------------------------ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
                              |||  |  | |  |  |||      || | |||  |     | ||  | |  |  | || |   | |||||  |  |   | ||| | |  || |||||||||| |||||||| ||||| ||||||||||||||||| |||||||| ||| ||||||||||||||||||| || ||||||||||| || ||||| |
gtcagtaacctactgttattttactatcttgtattttgagcccttctattcagttaattggatggtaaccatgtgctgta--aattgtttgttcattctca--ttctaaatctttatgtgcttcagATTAGGAAAATGAAGGGCTTGAAGCAGAAGAAGGCTCACCTCATGGAGATCCAGATCAATGGTGGTACCATTGCCGATAAGGTGGACTATGGATACAAGT

upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 4
--ggaagtaggtc--tatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
     |||    |  ||| ||  ||||| |      |   || | || |  | |   | | | |    |  |    | |  |  | | | |||||||  |  |||| |||||| |||||||| ||||||||||||| || ||  |||||||||| || || |||||||| ||  | |   | ||||||||||| |  ||||  |
cttatagtgttccaatatattaaatatagtccgtgttcagttttgttatgttaatataatggtttcgtggta----ttaaattgtttttctttgttttctgaagATAAGGAAGTTGAAGGGTCTGAAACAGAAGAAAGCACATTTGATGGAGATCCAAGTTAATGGTGGGACAGTAGACCAGAAGGTGGACTATGCATACAGCT

upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 4
ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacct-cttgtgta-tttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
     |   | |    ||  |  ||||  ||||| |   |  ||        |||  | | |      | ||  |    | ||| |   ||   ||||  |||| ||||| ||||| || ||||| |||||||| || ||  | ||||| |||||||| ||||||||||| |||||  | ||||||||||  |  ||||  |
--ccttctattttgtgtttgtcaaattccaaattcagagtccttccagttatcacatgatttagatatattcctaatagcctgtctggcttaaatcttacagATCAGGAAAATGAAAGGGTTGAAGCAGAAGAAAGCCCATATCATGGAAATTCAGGTTAATGGTGGTACTATTGCACAGAAGGTGGACTTTGCATACAGTT

upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 4
ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
    ||| || |   | |   ||    |   ||    ||   | |||||   ||||| ||  |  |  ||       |  | |||      |  ||  |||| |||||||||||||| ||||| ||||||||||||||| |||||||||| ||| |||||||||||||||||||  | ||||| ||||  | |||||  |
----gtaagtttgcttattgaatggaagtgtatatcataaactcttctg---cactacgttcttactgac-----aattctatgtgacctctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATCCAGATCAATGGTGGTACCATTGCCCAGAAGGTTGACTTTGCCTACAGTT

upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
             | |  ||| || || ||| || |  ||  ||||   |         | | |      ||| |   |   ||| |   | | |||||||| ||||| ||||| ||  |||| ||||||||||| || ||||  ||||||||| ||||||||||    || ||  | || || ||||| | || ||  |
------------gtatgccatttacttcaaa-ttcacaatcattttgcaaa--------tttcatttgtttctgattacgattgt-tggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT

upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0072g00340.t01 (Vitis vinifera), 3'ss of exon 4
ggaagtaggtctatctttcatataattgaaaattga-ttatttttttctgaggcactaggtattagccaactctcacct--cttgtgtatttgtt-tcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
     ||  |    |||    ||| || |||||| | ||     | ||  |  | |||  |  |    | |    | ||   || | |  |  |  | || |||||||||||||||||||| ||||| |||||||| || ||| |||||||||| |||||||||||||| ||||||||| | || ||||| || |  ||    |
----ttatttgacgcttgtcaatacttcaaaatttagttccagctctcatatcccctaaatgatccttatcctctaactaatttctctggtcatggtgttatagATTAGGAAGATGAAGGGATTGAAGCAGAAGAAAGCACACTTGATGGAGATCCAGGTCAATGGTGGAACCATTGCTCAGAAAGTGGATTATGCTTATGGTT

upper sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0035g01020.t01 (Vitis vinifera), 3'ss of exon 3
-----------ggaagtaggtctatctttcatataattgaaaattgattatttttt-tctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
             |   |  | |    |||| | | || |   || |   || |   |   ||  || |  |||| | || ||  ||  || | | |         || |||||||| || ||||||||  |||| ||||| ||||||||||| |||||||||||||| ||||||||     ||||| | ||||| ||||| | |||    |
gtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggca-ctgacatatcctatatggaatggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATTCAGGTGAATGGTGGAGATGTTGCTAAGAAGGTTGACTATGCCTATGGTT

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|28361753|gb|CB240109.1|CB240109
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATG
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATG
EST: gi|29167714|gb|CB410974.1|CB410974
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|21843251|gb|BQ703832.1|BQ703832
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211283996|gb|FL031550.1|FL031550
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|67014068|gb|CO442817.1|CO442817
EST:     AGAAGATGAAGAAAT-TGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|67021955|gb|CO450704.1|CO450704
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|19351800|gb|BM896332.1|BM896332
EST:     GAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGCAAGAAGGCTCACCTGATGGAGAT
genomic: GAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAG-AAGAAGGCTCACCTGATGGAGAT
EST: gi|60398332|gb|DN231148.1|DN231148
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211498695|gb|FL368204.1|FL368204
EST:     AGAAGATGAAGAAATATGCTTCTGGTATCCGTGTCATTGCTCATACCCCG                         G
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttag-
EST: gi|211498695|gb|FL368204.1|FL368204
EST:     AGAAGATGAAGAAATATGCTTCTGGTATCCGTGTCATTGCTCATACCCCG                         G
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttag-
EST: gi|9731775|gb|BE510527.1|BE510527
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|21987338|gb|BQ778866.1|BQ778866
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|31351952|gb|CD436309.1|CD436309
EST:     GAAGATGAAGAAATATGCTTCTGTTATCCGTGTCTATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
genomic: GAAGATGAAGAAATATGCTTCTGTTATCCGTGTC-ATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|84980280|gb|DW530629.1|DW530629
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|32851092|gb|CD990773.1|CD990773
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211473687|gb|FL374870.1|FL374870
EST:     AGAAGATGAAGAA-TATGCTTCTGGTATCCGTGTCATTGCTCATACCNAG                         AT-ANGAAAGATGAAGGGTTTGAAACAGAAGA-GGCTCACCTGATGGAGAT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAA-GATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGAT
EST: gi|213172548|gb|FM192996.1|FM192996
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCACACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|28873487|gb|CB329470.1|CB329470
EST:     GAAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGG
genomic: GAA-GATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGG
EST: gi|32855450|gb|CD995131.1|CD995131
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCATTATTATGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211490786|gb|FL398948.1|FL398948
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATT

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: 1577

TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1198

TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1037

TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 860

TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
                        ctctcac  putative branch site (score: 860)
                                       tatttgtttctttt  putative PPT
                                       tatttgtttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - -gcactag