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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA

Basic information

species Zea mays
transcript GRMZM2G704093_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 9
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatc-gttagatgcatctgaaatatcaata--tttctttatatagattcagtgcccttttaacatctctta--ttacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                                                          |||||   ||||||  || |  || |     ||||||  |  ||  ||||| | |||| | | | ||| ||| ||    |   ||   ||||| |   |||||||||||||||||||||||||||| || || |||| ||||||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||
----------------------------------------------------------tctatgcctctatccattggtggcgtacacgatatcatcaatttcttttatttggatttaatactcttgtaaaataaaatgactttggtgctgttctcagGACATTGAATTATCCAAAGAAATAAATGAGTCTTTCAAGCAATCATCTCAAGCAAGGACAAAGCTTCCATCTGGCATTGAAATGAGTGTTCACGTGCTTA

upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                                             | ||||| |       ||  | || |    |  | ||  |||| ||| | || |||||  ||      |||   |     |  |  ||| |     |  |   |  |||||||||||||||| ||||||||||| ||||||||||  || ||||| || || ||| |||| ||| | ||||| ||||||||||||||||||||  | |
--------------------------------------------atcttttgaatg-----atgatgctctgacaaacttca--tgaattatta-tagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaat-cagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA

upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 10
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctat-agttct-atcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                                                         || ||| |||| | ||  |  ||   |  | |   || | |||  |||| | |  || || ||   |||  |  |   |||||   |      |  |||||||||||||||| |||||||||||||| || ||||  || ||||| || ||||||||||| || || || || ||||||||||||||||||||  | |
------------------------------------------------------ggactatatgagttatgatgatctgacaaacttcatgaattactatagctttttttt-atccattgttttttataactacattattttttttctaattcagGACATTGAATTATCAAAAGAAATAAACGAGTCCTTCAAACAGTCATCCCAGGCTAGGACAAAACTCCCATCCGGGATTGAAATGAGTGTTCATGTTTTGA

upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 9
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                                                 ||       | | |  |  | |    |  | ||  |||| ||| | || |||||  ||      |||   |     |  || ||| |     |  ||  |  |||||||||||||||| ||||||||||| || |||||||  || ||||| || || ||| |||| ||| | ||||| ||||||||||||||||||||  | |
-------------------------------------------------ttattgttttgtgtgatgatctgacaaacttca--tgaattatta-tagttcttattaacatcacagcttctgacaactatgtctcaaattgttgtgaat-cagGACATTGAATTATCAAAAGAAATAAATGAGTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA

upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 9
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatc-tgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                                                     ||    |  || |  |    | | | || |  |||| ||| |    || | | |||   ||   |    |    || |   || ||   | ||  ||  |||||||||||||||| |||||||||||||| || |||| ||| ||||| || ||||||||||| || || ||||| ||||||||||||||||||||  | |
-----------------------------------------------------actatgccgtaatgatgatctgacaagctttatgaattattatagcttttatttatctgttgctttttataactacgttattttttttttcctaatt-cagGACATTGAATTATCAAAAGAAATAAACGAGTCCTTCAAGCAGTCATCCCAGGCTAGGACAAAACTCCCATCAGGGATTGAAATGAGTGTTCATGTCTTGA

upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                                   | | |||| |   |||| | |  || |||   | | | |   ||   | ||    ||  |||       || |  | | | |     |  |||||||  ||  |  |     ||  |||||||||||||||| ||||| ||||| || || ||||  |||||||| ||||| |||||||| |||||  |||| ||||| ||||||||||||||  | |
-----------------------------------aatgttatatgggtttgtaaatttccata---caagcttataatttgtttg---catagata-------atgttaaattattttttatgcaacatcttgtaacattt-----ttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA

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|32809761|gb|CD961995.1|CD961995
EST:     AAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAG                         GACATTGAACTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAA
genomic: AAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAA
EST: gi|31357483|gb|CD441840.1|CD441840
EST:     AAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAG                         GACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAA
genomic: AAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAA
EST: gi|31353844|gb|CD438201.1|CD438201
EST:     AAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAG                         GACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCT
genomic: AAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCT

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: 46 (upstream exon), 48 (downstream exon)
Score: 191

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 130

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAATAAGCTGGAGGGAATGTTCAAGgtagtgttag ... ctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
                       ttttaac  putative branch site (score: 138)
     tatatagatt  TA-rich tract