Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC

Basic information

species Zea mays
transcript GRMZM2G451716_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
aaagattatgaaggctaaatcttcgaatgcat-gcacgcttcataaa-tagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
         |  |  |  || |||  |||| | |  |  |  ||  | ||  |||    ||    | |   ||| | |  | || | |    | | |||||| | ||| |||||||||  |||||||| || || ||||| ||||| ||||||||||| |||||  |||| |||||||||    ||||  ||||||||||||
---------gttgtttggattttcttatgctttgagctatctatgtactatgaattttgggttcctcatgttgatggaactaaataaagaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
----------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
                             || || ||    | ||||  |   |   |||        || | | | | |   |    |||  || |    |||  |||  |        ||| ||||   ||  ||||||| |  ||||||||||||||||||||||||||||| ||||| || |||||| | || ||||| ||| |||||||  ||||||| ||||
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgc--aattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
----------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
                             || || ||    | ||||  |   |   |||  ||  |||| | | | |     |   | | ||  |||  |  |  |||  |      | ||| ||||   ||  ||||||| |  ||||||||||||||||||||||||||||| ||||| || |||||| | || ||||| ||| |||||||  ||||||| ||||
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacata-aca-ttcacagacacacgcatacacactgtactaatagactaacttatgatgc--atttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
----------aaagattatg-aaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtat----------aaaaatgaagaactttaacacatctg---tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
          ||   ||||| ||  |||| |      |   ||    | ||   |    ||  |     || | |          || | |  | |  | ||| | ||  |   | |  | ||| | |||||||||||||  |||||||| ||||||||||| || || ||   ||| || |||||  |||| ||||||||||| |||||  ||||||||||||
gttatttggaaacccttatgtaatactaatttgatataattatctgtgatttgaattctgagttcatctgattctttttgtttctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G17250.1 (Glycine max), 3'ss of exon 11
--------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaag-gagtataaaaatgaagaactttaacacatctg---tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
                     || | ||    |    |||  ||       || |  ||   |  ||   | |      |  | ||| | |  | |    ||| |  |  |   | |    ||| | |||||||||||||  |||||||||||||||||||| || || ||   ||| || |||||  |||| ||||||||||| |||||  |||||||||| |
gttagttggaaatccttatgtaatactaatttgatataattatctgtgatctgaattctgagttcatctgattctttttgtttctaagagtttatatgcctaataattaaggaatattgcacagGCTTTTCATGGGAAAAAATGGGAGAAATTCAACAGTGAAAAGGTAGCGGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTTC

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaa--tagaaatggaaggagtataaaaatgaagaactttaacacatc-tgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
                                               | ||   ||||  ||| ||||   |  |   |   |||||||     | ||  ||    |  | | ||     ||    ||   ||| | | | |  ||| ||||  |||| |||| ||||||||| |||||||||||||| ||||| || ||||| |||||| |||| ||||||||| | |||||  ||||||||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaagg--aaagcttcttgtctacaga-atttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaa---tagaaatggaaggagtataaaaatgaagaactttaacacatc-tgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
                                              || | | || |  ||| ||||   |  |   |   |||||||    || || ||  | |    | | ||     ||    ||   ||| | | | |  ||| ||||  |||| |||| ||||||||| ||||| |||||||| ||||| || ||||| ||||||  |||  |||||||| | |||||   |||||||||||
gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaagg-aaagcttcttgtctacaga-atttcataaggtctacaactgatatggac-tgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC

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|78073984|gb|DV502418.1|DV502418
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
EST: gi|5895966|gb|AW037212.1|AW037212
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
EST: gi|5895962|gb|AW037208.1|AW037208
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
EST: gi|213191920|gb|FM183353.1|FM183353
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
EST: gi|76928188|gb|DV171510.1|DV171510
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGGCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
EST: gi|31358340|gb|CD442697.1|CD442697
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGT
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGT
EST: gi|71301676|gb|DR786905.1|DR786905
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
EST: gi|91048864|gb|EB159282.1|EB159282
EST:     ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG                         ACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA
genomic: ATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCA

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: 311

AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 102

AATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAGgtgagattct ... tctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
                               ctttaac  putative branch site (score: 102)
                                         tctgtctctt  putative PPT
                tataaaaatgaagaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - tgaaggc
- - - - - - - - - - - - - -tgcatgc
- - - - - - - - - - - - - - - - - - gcttcat
- - - - - - - - - - - - - - - - - - - - - - aatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacat