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

gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG

Basic information

species Arabidopsis thaliana
transcript AT2G20100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G083749_T02 (Zea mays), 3'ss of exon 4
gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
                                      | || |  | | | ||  |||     |  |     |||||| |   ||||  |||| |   |   |||| || ||||||||||| ||||| ||| |   |||| ||||||| ||||||||||||||||  |||||||| |||
-----------------------------------cactgaaaacaagcaagtccctgacatgcatatatgc-atattacttgttgtt--gttgttgtttttttttttttgcagactgacactgcctccgtcctacagGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG

upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G083749_T05 (Zea mays), 3'ss of exon 4
gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
          | |  || | |    | | | || |   | || |  | | | ||  |||     |  |     |||||| |   ||||  |||| |   |   |||| || ||||||||||| ||||| ||| |   |||| ||||||| ||||||||||||||||  |||||||| |||
----------ttaggaggtgcgcggagtga-caatcactgaaaacaagcaagtccctgacatgcatatatgc-atattacttgttgtt--gttgttgtttttttttttttgcagACTGACACTGCCTCCGTCCTACAGGAGACTATTGGCTACATTAGATTCCTCCTGAGTCAAATCGAG

upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G09180.3 (Glycine max), 3'ss of exon 3
gtataattactgattagttccctttactaatcacttgt-ttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
 |||  |     |  |      ||   | ||  | |   |||| ||  | |||   |||| |   |||    || |          || |||   |||  || |||||    ||||||||||| |||||||||||||  || |||||||| || || |||||||| || ||||||||||||
-tattttacagaagaaaaagggttcgtttatagcataaattaaaatattataaataatgagtgggaataacgttgtg---------gtgtggcatatt--tcacttttg---cagACTGACACGGCCTCTGTCTTGTTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG

upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G35610.1 (Glycine max), 3'ss of exon 4
gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
        |   ||   | | || |  | | || ||   ||  |      ||   |||| |   |||   | | || |      |  ||  ||  ||  |   |  | || ||||||||||| || |||||||| |  || |||||||| || || |||||||| || ||||||||||||
--------aacaat--atgctctctgtttagca-ttacatagaagag---aagagatgactgggaatatgactgtagtgtgtggtaattttttatttattttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGCTATATCAGATTCCTTCAGAGTCAAATTGAG

upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 4
gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggtt-gattgatccctt-ttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG----------------------------------
                 | | ||||  | ||      ||  | |  |   ||   |||| | | |||   | | || |      | | |  || ||||  |   ||  | || ||||||||||| || |||||||| |  || |||||||| || || |||||||| || ||||||||||||                                  
----------------atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT

upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G04110.2 (Glycine max), 3'ss of exon 4
gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggtt-gattgatccctt-ttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
                 | | ||||  | ||      ||  | |  |   ||   |||| | | |||   | | || |      | | |  || ||||  |   ||  | || ||||||||||| || |||||||| |  || |||||||| || || |||||||| || ||||||||||||
----------------atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAG

upper sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 4
gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
              | ||||||    |   |   || |||    || ||  |  ||   |  |       || |  || |    |  | |  || ||  |  || || || |||||||||||||| ||||||||||  || |||||||| || || ||||||||||| ||||||||||||
-------------atggttcccccccccctttttttttttttttttttcagaaataaagaagacgtgaatatgactttggagggttgtggtgtggtttttttctctt-ttgcagACTGACACAGCTTCTGTCTTGTTAGAAGCTATTGGTTATATCAGATTCCTCCAGAGTCAAATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaaattgaattatattagtcactgtttggttgattgatcccttttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG
                                  gattgat  putative branch site (score: 4)
                                        tcccttttatttc  CT-rich tract
     aattgaattatattag  TA-rich tract