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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacaacgtaaatgtaaaaaaaaaacatatgtaagatgcaagatttgttgttctgagttagctgcggcttcatcttgtccccccccccttttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG

Basic information

species Zea mays
transcript GRMZM2G121262_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------------------------------------gcacaacgtaaatgtaaaaaaaaaacatatgtaagatgcaagatttgttgttctgagttagctgcggcttcatcttgtccccccccccttttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG
                                                                                                   | | |  ||   | | || || |   ||||| ||||||||| |   ||   | ||||      |   | | |||||  |  |  |   ||   ||  |||||||| | ||| ||||| ||||| |||||||| |||||||||||||||||||||||||||||||||
gtgagaaggggggttgatcttacacactaaaagaaatgtaaaaaaaaaatctatgatgtttgagggacaacagattcattcgctgagaaaaatatcaatgaaaacagttggtttgaataacatg-atatggaagatgcaaaaaaggtaagtatgaga-----gtaaccttatctttgcatcttctttttccttgagcagGTCACGAAGCAGCACAATGAAGAATGTAAACGACTATTAAGACTTATGGGGGTTCCTGTTGTAGAG

upper sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 7
gcacaacgtaa-atgtaaaaaaaaaacatatgtaagatgcaa---gatttgttgttctgagttagctgcggcttcatctt-gtccccccccccttttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG
  ||| | ||   | |   ||       |||      || |    ||  ||  | |  ||  |   | |  |   |  |   |   |  | |||| | |   ||||| |||| |||||||||||||||||| |||  ||| |||||||| ||||| || |||||  | |||
--acagcatattgtttttcaactttctttatacccagtggagattgacatgaaggttagaactgtttacttcagtacttccattttctgctccttgttt---cagGTGACAAAGCAACACAACGAAGATTGCAAAAAGCTTTTAAGACTGATGGGAGTGCCTGTAATTGAG
















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|88749646|gb|DY533787.1|DY533787
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|28568845|gb|CB280720.1|CB280720
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|148983038|gb|EE028944.2|EE028944
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|26558947|gb|CA831182.1|CA831182
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGACTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|30087247|gb|CB885455.1|CB885455
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|50328745|gb|CO523871.1|CO523871
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|148945123|gb|EC890320.2|EC890320
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|78117503|gb|DV535890.1|DV535890
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|5566733|gb|AI881599.1|AI881599
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGACTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|148985935|gb|EE029848.2|EE029848
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|89763728|gb|DY690807.1|DY690807
EST:     GTAGGAGATAAAGATGCGATTGANAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|22473079|gb|BU037559.1|BU037559
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGACTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|31405508|gb|CD484240.1|CD484240
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|18661475|gb|BM501417.1|BM501417
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGACTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|87156101|gb|DY400890.1|DY400890
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGACTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|71444731|gb|DR825781.1|DR825781
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|74235361|gb|DT643275.1|DT643275
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|9952839|gb|BE639422.1|BE639422
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|93014006|gb|EB639526.1|EB639526
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|76018920|gb|DT946090.1|DT946090
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|32907157|gb|CF011970.1|CF011970
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|91054792|gb|EB165210.1|EB165210
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|60349759|gb|DN216732.1|DN216732
EST:     TAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
genomic: TAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGG
EST: gi|211017549|gb|FL416074.1|FL416074
EST:     GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAG                         GTCACAAGGCAACACAACG
genomic: GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACG

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: 277

GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 31

GTAGGAGATAAAGATGCGATTGAAAAATTGAGCAAGAGGACTGTAAAGgtaatttctt ... ttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttctgagttagctgcggcttcatcttgtccccccccccttttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG
                      cttcatcttgtccccc  CT-rich tract
                                           ttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacaacgtaaatgtaaaaaaaaaacatatgtaagatgcaagatttgttgttctgagttagctgcggcttcatcttgtccccccccccttttatggacagGTCACAAGGCAACACAACGAAGATTGTAAACGGCTATTAAGACTTATGGGGGTTCCTGTTGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
gcacaac
- - - - - - - -aaaaaaa
- - - - - - - - - - - - - atatgta
- - - - - - - - - - - - - - - - - -atgcaag
- - - - - - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcgg