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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattgattgacatcagggcatctaagctcgtttttgtatgtagtgaagaaataaagacctatggctttacttttctaatttgattttactgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 3'ss of exon 1
---caattgattgacatcagggcatctaagctcgtttttgtatgtagtgaagaaataaagacctatggctttacttttctaatttgattttactgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT
   |   |||  |  || | |  ||  |  |      || ||  |  ||   ||  ||| ||||     | |||| | |||||| | ||||  ||  | |||||| |||||||| ||||||||||||||||  || || ||||||||||||||||| |||| |||||||||||||||||| || ||||||||||||||||| |
atacgcgtgaa-gctattatgaaatgaagaccttccattttaattgttgtcaaatgaaaaaccttgcaatctactct-ctaattcgttttttgtgcct-gcagGACTCTCCTGTCTTCAATTTCATCAACAGCCTATCTCCTATACCACCACCTAAGCCTTCAGACTCAGCACATAATGTTCAACTATTCAAGTCATCAGACT

upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0030g01800.t01 (Vitis vinifera), 3'ss of exon 1
---caattgattgacatcagggcatctaagctcgtttttgtatgtagtgaagaaataaagacctatggctttacttttctaatttgattttactgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCT-ATTCAAGTCATCAGATT
    |||  |||  | || |   ||      |  ||| | | |    |     | |       || ||   | |  |   ||       |||    | |||||||||||||||| || |||| |||||||| |||||| |||||    |||   ||  |  ||  | | |  ||  |  | ||||| | | |  |   ||  | 
ttgaaatctattctcttctgatgattc---tttttttatttttcccattgcttagtgggtttataaggtcatgccctaaaaaacaatccttatccatatgcagGATTCTCCTGTCTTTAATTACATCAACAGTCTCTCACCTATTAAGCCAGTCAAGTCCATACCCACTGATCA-GACATTCAGCTCACTTAGTTTTGCATCTC
















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|211366534|gb|FL297817.1|FL297817
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|87152637|gb|DY397426.1|DY397426
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211513604|gb|FL043440.1|FL043440
EST:     ATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCG-CGGGTTTCCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACC
genomic: ATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGG-TT-CGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACC
EST: gi|211366529|gb|FL297812.1|FL297812
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366525|gb|FL297808.1|FL297808
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|87152122|gb|DY396911.1|DY396911
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366538|gb|FL297821.1|FL297821
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|19437165|gb|BM953575.1|BM953575
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366527|gb|FL297810.1|FL297810
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366530|gb|FL297813.1|FL297813
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366524|gb|FL297807.1|FL297807
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|71312702|gb|DR792875.1|DR792875
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366536|gb|FL297819.1|FL297819
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366537|gb|FL297820.1|FL297820
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211369184|gb|FL297822.1|FL297822
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211363879|gb|FL297806.1|FL297806
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211363877|gb|FL297804.1|FL297804
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366531|gb|FL297814.1|FL297814
EST:     AGATGGACACGCCGGATAGGCCTCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366532|gb|FL297815.1|FL297815
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|211366526|gb|FL297809.1|FL297809
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|22491113|gb|BU051036.1|BU051036
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
EST: gi|22490856|gb|BU050779.1|BU050779
EST:     AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAG                         GATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT
genomic: AGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCT

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: 416

CGGCGGGGAGGGAGACAGATGCGGGAGGCCCACCGCGGGGTCGCCGGACCAGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

CGGCGGGGAGGGAGACAGATGCGGGAGGCCCACCGCGGGGTCGCCGGACCAGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

CGGCGGGGAGGGAGACAGATGCGGGAGGCCCACCGCGGGGTCGCCGGACCAGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

CGGCGGGGAGGGAGACAGATGCGGGAGGCCCACCGCGGGGTCGCCGGACCAGATGGACACGCCGGATAGGCCCCGCGCCGGCGCCGGCGCCGGGTTCGAGgtcctccatc ... tgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaaataaagacctatggctttacttttctaatttgattttactgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT
                                       ttttact  CT-rich tract
                     tttacttttctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattgattgacatcagggcatctaagctcgtttttgtatgtagtgaagaaataaagacctatggctttacttttctaatttgattttactgttttgcagGATTCTCCTGTGTTCAATTTCATCAACAATCTCTCGCCTATACCACCACCTAAACCTTTAGACTCAGCACATAATGTGCAGCTATTCAAGTCATCAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- -ttgattg
- - - - - - - - gggcatc
- - - - - - - - - - - - - - - - - ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - - -aaataaa