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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC

Basic information

species Zea mays
transcript GRMZM2G158479_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 6
---gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
      |  | || |    ||  |    || || |  ||        ||  |  ||   | | | ||   |    ||||  || ||||| ||||| || |||||| ||||||||| |||| |||||||||||||||||||||||||||||||| ||||| ||||||||||  |||||||||||||| ||||| |||||||| |
gttatttttctagctgtaatttttcaagctggttgtgttctgttatttgctttctgcagtgt-gcaac--attagtaaactctctggttgatttgtattctagATCCGTGAGGGTTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 5
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttg------catcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
    |   ||  |   ||  | |  | | | | |  |  | | |||  |  || |||   ||  | ||||| |     | | | | | ||         |   |||||  | ||||| || || || ||||| ||||| |||||||| || || |||||||| || |||||||||||||| ||||| || ||||| |||||||| |
----atttagtactagttcatatatcattttgtccctataccgatg--tactgatattgtgttcttaaacctttttttcatggctatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 5
gcataccaaggtcaccttggtt-tgccttgtcgcctttgaaacc----atggctcttgttatctcgtaatcaaaccataaa----aactttggttt----atttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
             | |||  || | | || ||  ||||  |       |    |||   ||| | | | | |||    |||     | | |||||     | |   |   |||||| | || || |||||||| ||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||| ||||| |||||||| |
-------------aacttaattatactttctcaactttctagttctcaacaaatctaaatatattgcacttaaagtgaaaattttgattatggttctctaaataataatgtagATTAGAGAAGGACTGCACTATAATCCTTATTTTCCTGGCGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGTGCTGTTGAATATGAAGATGGTACCC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatg-gctcttgttat-ctcgtaatcaaaccataaaaactttggtttatttg-catcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
   ||    |  |   ||  | |  | | | | |  |  | | |||  ||  | || |  || ||| |      | |  ||| || |  |  |   |   |||||  | ||||| || || || ||||| ||||| |||||||| || || |||||||| || |||||||||||||| ||||| || ||||| |||||||| |
---tatatggtactagttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 5
--gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
   | ||   |      ||    ||  ||  |   |    || | |    | |||  |  |       |||     |    |||  ||||     |   |||||| | || || |||||||| ||||| || || |||||||| || || || ||||| || |||||||||||||| |||||||| ||||| |||||||| |
gaacttaattatactttctcaactt-tctaattctcaacaaatctaaatatattgc-acttaaagtgaaaatttcgattgtttttttttaaaaaaaatgtagATTAGAGAAGGACTGCACTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
       ||  || |     |||    | | | ||| |  |  |   ||     |   | | | | | |  |  ||  || ||  | |   | |    ||||  | ||||| || ||||||||||| || ||||||||||| || || || ||||| || ||||| || |||| |||||| || ||||| ||||| || |
----gtaaatttctctcctatttttgctttagactt-gttattacaacttcaaattgttggaagttaga--aataatcctgtgactaacgggtac---agATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 5
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtt-tatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
                |  ||||  ||  |    ||  | |       ||||   ||        |     || |||| |  | |  ||  || |    ||||| | |||||  | ||||||||||| || |||||||| || || || || |||||||| ||||| ||||||| ||||||||||||||| ||||||   |
---------------gtaagtttctctcatt---ttccacattgaacttcttcgaattcaaagtgctggttatgaaaaatccgatgataactgtac---agATTAGAGAGGGGTTACACTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
gcataccaaggtcaccttggtttg--ccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaa---ccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
     | |   ||| ||||  |||    |||||  | ||  |        |  ||   |||  |||| ||    ||||    |  |   |  | |       |||||||| || || |||||||| ||||| || ||||||||||| || ||||| ||||| || ||||| |  ||||| |||||||||||||| |||||||| |
----ccgataatcatcttgacttgggttttgtcatcatttga-ttgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 5
gcataccaaggtcaccttggtttgccttgt-cgcctttgaaaccatg--gctcttg-----ttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
         | | |  ||  |||   || |  |  | || |   ||   | || ||      |||  |   | | || ||   ||  | |     | |    |  ||||| || || ||  ||||||||||||| ||||||||||| ||||| || || ||||| || ||||| | |||||| ||  |||||||||| |||||||| |
--------tgctgatttttttttattttttatgtttatggacatattctgttcatgatgacctattcctctacctaatcaatcaagttgttcacaaatatttttgtagATCCGAGAAGGGTTGCACTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGC

upper sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
lower sequence: EDO96204 (Chlamydomonas reinhardtii), 3'ss of exon 7
gcataccaaggtcaccttggtttgccttgtcgcctttgaaa--ccatggctcttgttatc--tcgt-aatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
     |  |  | | | ||  |        | ||   ||    | |   || | || |    || | |||  |||| | |            |   | | |  |||| || ||||| ||| ||||||| ||||||||||| || || ||||| |||||||| ||||||||    || || | ||| ||||| ||||| || || |
----tcttaattaatcatgaatgtaaccccccccaaagagggtctaccactttcgtaactaatcatgaatgcaaccctcaccctcaaccgccacccgga-cgcagATCCGCGAGGGCCTGTACTACAACCCCTACTTCCCGGGCGGCGCCATCGCCATGCCCAAGATGCTGGTGGACGGCGGTGTGGAGTACGAGGACGGCACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC
                                       tttattt  CT-rich tract
                          ataaaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaaccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG