Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

Basic information

species Zea mays
transcript GRMZM2G168228_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgc---ccttgtttt---tagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                  | | | |  |  ||||    |  ||||  | |   |     || || | || | | ||  |||||| |      ||||| ||   |||||||||||||||||||| ||||| || |||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||| |||||||
----------gtaagtaaattgtaattgatcaat-cacaacgcctttctg--aattccctgtgatgtttgctttctagtttatcttcttcatcttgtgttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
--acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
  |   |||  || | |    ||   |   |  |  || |  |   |||           ||   |    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
tgaagaactaaacatttaaatctcatattttttatggtagctactatgg--attttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
acttactccacctctgggactttgaacgtccaatgtggagagcctgg--cagccgaggaggtgggaggctttcctgctcat-ttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                |   |||| |     |||||    ||  ||   ||    |  || ||  |       | |   |   ||   || | |  | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | ||||
------------gtaagccttttgtata---aatgttcttagtttgtatcaattcaacagctgaaaaataaatcagtgaaaactagtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
acttactccacctctgggactttgaacgtccaatgtggagagcctgg--cagccgaggaggtgggaggctttcctgctcatttatcc-tgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                |   |||| ||    |||||    |   ||   ||    |   | ||  |       | | | |    |   || | |  | | ||||||||| |||||||||| ||| |||| || ||||| || ||||| |||||||| |||||||||||||| || |||||||||||||||||  |  | ||||
------------gtaagccttttgcaca---aatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaaaacttgtatggcttcttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 19
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
              |  | |||| ||| |   | | | |  |  | | |   ||     |||  |            |  | | ||  | ||||||  |||||||  ||||||||||  |  |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
-------------gtaagccttttaactt---aagggtattgttttgta-ttgattcattggatg-----------taactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGTAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACGA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 22
-acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
     ||   | |  |   |  |  ||  |   |||   ||   ||   |         ||   |    |   || | |||| |  || |  |  |   |||||||| | ||| | || || || || |||||| | || ||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||||
tgaagacctaaacatttaaatctccaattttttatg-atagctactatgaattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTAGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgagga------ggtgggaggctttcctgctcat--ttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                     |  |||||   | || |||       | ||    | ||   ||   ||   | | ||  | ||||||  |||||||  ||||||||||  || |||| ||||| ||||| ||||| |||||||| |||||||||||||| || |||||||| ||||||||  |  | || |
-------------------------------------gtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagctttgtttc-agGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccga--ggaggtgggaggctttcctgctcatttatcctgc-----ccttgtttt-tagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
         |  | ||   ||    ||||  |     |    | |  | |   |    || |        || |||   || | |    |     |    || | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| ||  |  | ||||
------atgaggtatgttgct--agacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccga--ggaggtgggaggctttcctgctcatttatcctgc-----ccttgtttt-tagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
              |  |    |  ||||  |     |    | |  | |   |    || |        || |||   || | |    |     |    || | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| ||  |  | ||||
-------------gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
acttactccacctctgg-gactttgaa---cgtccaatgtggag----agcctggcagccgaggaggtgggaggctttcctgctc-atttatcctgccc--ttgtt-tttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
         |  | ||  ||  || ||   ||| |  |||        | | | | ||||       |      |||||  | ||   | ||  ||     |  || || |||||||| |||||||||| || || || || || || ||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||| | |||||||
-------gtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
---------------------------------------------------------------------------------------acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                                                                       |  |  || | |  |   | || |    ||  || |  ||   ||  |  |       ||   |   |||  || | | |||   |    ||||||  |||||||  ||||||| || || || || || || |||||||||||||| ||| |||| ||||| |||||||| ||||||||||||||||| ||  | ||||
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaa-ttcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatt--tattgtttc-agGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA

upper sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatt-tatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                      ||| | ||  || |        | |      |    ||  |   | |  |||||   | ||| ||    ||| | |||||||||| ||||| ||||  || ||||||| || || |||||||| |||||||| ||||||||||| || |||||||| |||||||||||  || | ||||
---------------------gtgagcttc--atataactctttttgtt-tatatattgtttgcttcctctctgcttgctatattctttgtttggtcttagGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA

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), 49 (downstream exon)
Score: 94

GTCAGAAATCCAGCAAGATTCATGCAAGATGTGCTCTGCCGTTGAACGGAACCAAGCATGCTCAGGAATACCTCTAATTTCAACATCTCAGTGTCCGGATgtgtgaacct ... ttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 98

GTCAGAAATCCAGCAAGATTCATGCAAGATGTGCTCTGCCGTTGAACGGAACCAAGCATGCTCAGGAATACCTCTAATTTCAACATCTCAGTGTCCGGATgtgtgaacct ... ttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GTCAGAAATCCAGCAAGATTCATGCAAGATGTGCTCTGCCGTTGAACGGAACCAAGCATGCTCAGGAATACCTCTAATTTCAACATCTCAGTGTCCGGATgtgtgaacct ... ttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

GTCAGAAATCCAGCAAGATTCATGCAAGATGTGCTCTGCCGTTGAACGGAACCAAGCATGCTCAGGAATACCTCTAATTTCAACATCTCAGTGTCCGGATgtgtgaacct ... ttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
                                     tcctgcccttgttttt  CT-rich tract
                                             ttgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccgaggaggtgggaggctttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - -ctccacc
- - - - - - - - - - - - - - - caatgtg
- - - - - - - - - - - - - - - - - - - - - - - gcagccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctgcc