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'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC

Basic information

species Zea mays
transcript GRMZM2G058910_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 10
--cttatatc--ttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
   |   ||    |    | |||  | |  |   | |    ||||   ||||   ||| |  ||   ||    || ||||||   ||| || ||| || |||||  ||||||| |||||||||||||| ||||| |||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| ||||||||||||
aattagcattgactcctgaaaaatcaataaagagcttgctgtttg---tttgggccaa-atggtttagttaggaactgctaactttgtattacatctgatacagGATAGCCAAATATCAAGAAGCAAACCCTGGTGTATTCACTATTGTCACTTTTCCTTTCTTATTTGCTGTCATGTTTGGAGATTGGGGACATGGAATTTGC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 10
cttatatcttgtaaataaagaa---gtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgcta-atgatgtgttccatgtgg----tacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
       ||   || | |||||   || | ||| || |  |||    ||| | |   || | | |  |  || | |  || |       ||  ||        | ||| || || |||||||| || |||||||||   || |  ||  | || || || || ||  | |||||||| ||||||||||||||||| |||||||| || 
------cctaacaatttaagaacttgtttcatt-atttgttttttacttttattttttatt-tgaaatatatcaatcttatacttcaacttttatactaacatttcagGGTTGCTAAGTATCAGGAGGCAAATCCTACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGGCATGGAATATGT

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
-cttatatcttgtaaataaagaagtgtaattcatatcat--ttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
 ||  |   || || ||    |  |  || |  | || |  |||    |||| | | |  |     |    ||| | | ||| ||   |   |  ||  ||||  | |||||||| || ||||||||||| || |||| ||| ||||| || || || ||| | |||||||| ||||||||||| ||||| ||||| || |||
actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaact-caaataatcgttaatacttg--acagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 10
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgcta-atgatgtgttccatg----tggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
 ||||   |   || | ||||| |    ||  |||  |||    ||| |||      | | |  |  || | |  || |   |   ||  ||     |  | ||| || || |||||||| || ||||||||    || |  ||  | || || || || ||  | |||||||| ||||||||||||||||| |||||||| || 
-ttattcttaacaatttaagaacttgttttgctatttttt----ttttacttttatttttgaaatatatcaatcttatactttaacttttatactaatatttcagGGTTGCTAAGTATCAGGAGGCAAATCCGACTGTGTATACTGTAGTTACCTTTCCATTTCTTTTTGCTGTAATGTTTGGTGATTGGGGTCATGGAATATGT

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
---cttatatcttgtaaataaagaagtgtaattca-tatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
   | | | |    ||  | |     | |  | || ||||  ||   ||| |  |   |    | |  |  ||   |  |     | || ||  |    | |||||| ||||| ||||| || || |||||| | |||||||| ||||| || ||||| ||| | |||||||| ||||||||||| ||||| |||||||| |||
caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttc----tttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
---------------------cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatac--tgtaaggtggata--agtgctaatgatgtgttccatgtggt-------acagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
                      | |     | |||  || |     |     ||| | |||||  | | |   |||    ||||   ||  |   | |  |      || | | |||   |        |||||| ||||||||||| ||||| ||||| || |||||||||||||| || ||||| ||| | || ||||| ||||||||||||||||| |||||||| |||
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 10
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggt-ttgactcaatactgtaaggtggataagtgctaa--tgatgtg-ttccatgtggt-acagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
    ||| ||      |   |  ||   ||||| |   |   | | |  | | || |   |    ||  | | | ||||  | ||||| |||||| |  |  ||| || |||||||||||||| ||||||||||| |||||||| ||||| || || || ||  | |||||||||||||||||||||||||| |||||| | |||
----tattttactttaacctatttgattttcattttgctgatgatatcaaattaacagaattgtttgcctca-tactaaaattatgtgattccatttaattgcagGGTGGCCAAGTATCAAGAGGCAAATCCTGGTGTATTCACTATTGTTACATTTCCATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 10
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatg-tggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
 |  ||| ||  ||||      |    ||  |  |  || |     ||  | | |    | |     |||   |  |   |    ||| ||  |  | ||| || ||||||||||| ||||  |||||||| |||| |   ||| | || ||||||||| | |||||||| |||||||||||||||||||||||||| |||
ttgttatttttcaaatggtattgccctatagaagtacttggctaaatgtttaagtggcatcatcca-atagtagagatcaactaattcaataatatttcagGGTGGCCAAGTATCAGGAAGTGAATCCTGGTGTATACGTGATTATTACATTCCCTTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaata--------ctgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
                                 | | |    ||   | | ||    |  ||   |    |   || |||    |||         |  |    |   | ||| || || |  ||||     |  | |||||| |    |||||| |||||||||||||||   || |||||  | |||||||||||| |||| ||||| ||||||||||| ||||| |||||||| || 
gtaagtgtgcagatcaacgatattacgacgcgttgaaactgggttgttgatgatcgctgttttcaactgctaagggattgtggtaatggttgttttcctttctttcattcagttctgatcagatgttgtgaata-tgcagTGTGGGACGGTATCAGGAAGCAAATCCTGGATGTTTTACCATAATAACTTTCCCTTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGT

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ10256 (Selaginella moellendorffii), 3'ss of exon 9
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
                                           ||  |  |    ||  | |  ||| | ||| || ||| | | ||    |   | |||||| |  |  |||||||||||||| || ||||| |||||||| ||||| || || ||  |||| || ||||||||||| || ||||| || ||||||  |
-------------------------------------------gtaagcttgtgaaccattat-tggctgagt-cttatggtctttt----ggtctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGAGACTGGGGTCACGGAATTGTC

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtt-tgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
                                       | || || |||  || || ||   | ||   ||   || ||| | | ||    |   | |||||| |  |  |||||||||||||| || ||||| |||||||| ||||| || || ||  |||| || ||||||||||| || ||||| || ||||||  |
--------------------------------------gtaagattgtgaaccattattg---gctgacaaaagtcttatggtctttt----ggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC

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: 212

GCTCAATATTTCAAGTTCTCAACACAAAAGAATCTCCTCCAACATATTTCCAGACAAATAAATTTACTTCAGCGTTCCAGGAAATTGTTGATGCGTATGGgtacgttttc ... tgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

GCTCAATATTTCAAGTTCTCAACACAAAAGAATCTCCTCCAACATATTTCCAGACAAATAAATTTACTTCAGCGTTCCAGGAAATTGTTGATGCGTATGGgtacgttttc ... tgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

GCTCAATATTTCAAGTTCTCAACACAAAAGAATCTCCTCCAACATATTTCCAGACAAATAAATTTACTTCAGCGTTCCAGGAAATTGTTGATGCGTATGGgtacgttttc ... tgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 475

GCTCAATATTTCAAGTTCTCAACACAAAAGAATCTCCTCCAACATATTTCCAGACAAATAAATTTACTTCAGCGTTCCAGGAAATTGTTGATGCGTATGGgtacgttttc ... tgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC
                           tgctaat  putative branch site (score: 475)
                              taatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatatcttgtaaataaagaagtgtaattcatatcatttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - aaataaa
- - - - - - - - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt