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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccggtttttgattcatctaaactgtttgtttgttcgatctag

Basic information

species Arabidopsis thaliana
transcript AT5G60920.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g32110.4 (Oryza sativa), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaat--attaggccttgtttaccggtttttgattcatctaaa--ctgtttgtttgttcgat-ctag------------
| || ||||||||||| |||||| | || ||||| || || |||||||| ||||||   |||||||||||||||||||||||||||   | | ||   |  | |||||  ||   |  |||||            || |||||  |   |||||          |  |||            
AGGCTTATGATGCGCTGGATCCAAATGGAAACATCACGATAAAATGGGACGTTATGTCGTGGACTCCTGATGGCTATGTTgtaagtagca-accccacaccaaaaaatgcatcttgtattgttcgttcaaaaa-aatccatctgcatcttgtttccccaactattattaggccataatttta

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g32110.2 (Oryza sativa), 5'ss of exon 1
--------------------AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaat--attaggccttgtttaccggtttttgattcatctaaac--tgtttgtttgttcgat-ctag------------
                    | || ||||||||||| |||||| | || ||||| || || |||||||| ||||||   |||||||||||||||||||||||||||   | | ||   |  | |||||  ||   |  |||||            || |||||  |   |||||          |  |||            
TTTTTGTTTTCCTCTTGCAGAGGCTTATGATGCGCTGGATCCAAATGGAAACATCACGATAAAATGGGACGTTATGTCGTGGACTCCTGATGGCTATGTTgtaagtagca-accccacaccaaaaaatgcatcttgtattgttcgttcaaaaa-aatccatctgcatcttgtttccccaactattattaggccataatttta

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggcc------ttgtttaccggt--ttttgattcatctaaactgtttgtttgttcgat-ctag------
|||| |||||| |||| |||||| | || ||||| ||||| |||||||| ||||||   |||||||||||||| || |||||||||   | | ||   | | | |  | | |   |      || || | || |  ||||  || ||  ||| ||| |     | | |  |||       
AAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTTgtaagtagcacatccatcattcgtatctttcatctcaacctattattgagcgataattttattttatagaaattgtcttgcaatgcaaaactaatagtat

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccggttt-ttgattcatctaaactgtttgtttgttcgatctag--------------
| || |||||| | || |||||| | |||||||| || || ||||||||||| |||   ||||||||||||||||||| |||||||    |   | | |    || || |    | || ||| |   |       | ||| || ||| | |  || | | | ||                
ATGCTTATGATTCCCTGGATCCAAACGGCAACATCACGATAAAATGGGATGTGATGCAATGGACTCCTGATGGCTATGCTgtaagtagcggtggcagtacaccaacatctctacctttattttcgtctcaacctgtacatttacactatcttgttctactacctctaataaaaaaatata

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM5G826714_T02 (Zea mays), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaaga---acctga--agtagaaaatattaggcctt--gtttaccggtttttgattcatctaaactgtttgtttgttcgatctag--------
| || |||||| |||| |||||| | |||||||| || || ||||||||| | |||   |||||||||||||| ||||| ||||||  ||     |||  |  ||  | | |||||    ||   |  || | |    || |  ||   |     | ||    |||| ||          
AGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTCgtaagtagaatgcccaccccaacagctgtatatatttcatctccagcctagcaggccctggtctattctattgagtagtccagtcgacctgtacaatata

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G08830.1 (Glycine max), 5'ss of exon 1
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagt-----tcaagaacctgaagt-agaaaatattagg-----ccttgtttaccggtttttgattcatctaaactgtttgtttgttcgatctag------
|||| |||||||| |||||||||   ||||| |||||||| ||||||||||| || ||||||||||| || |||||| ||||||||     |||    | | | || ||||| || ||||     | || | |   |  ||||||  ||| ||| |||     |  || |   ||       
AAGCCTATGATGCACTTGATCCAATTGGCAATATTACAATCAAATGGGATGTCATAAGCTGGACTCCAGACGGCTATATTgtaagtgatcatcactttcttaatgtgagaaagtactaggaaaaacattatattgtgagttttga--catttaatctgaaaagtattttggagtaagaaata

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G06660.1 (Glycine max), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaa------aatattaggccttgtttaccggtttttgattcatctaaactgtttgtt-tgttcgatctag----------
   | |||||| | ||||||||| | || || || ||||| ||||||||| |||| |||||||| ||||||||||||||||||||| ||      |  | |          ||||| ||       | | | | ||||   | ||  ||  || | ||| |    | | | |          
---CTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTTgtaagtccattcttttacaatgtcgcctattaatatcagaagcaaataatctgatttta--taattaaacatgatggttctaaatgtttttggctctttttc

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G00210.1 (Glycine max), 5'ss of exon 1
--------------------AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccggtttttga---ttcatct--aaactgtttgtttgttcgatctag----------
                    ||||  ||||||| |||||||||   ||||| |||||||| ||||||||||| || ||||||||||| || |||||| ||||||||      | ||    ||         || | || | |   |  ||||||   || | ||  |||   |||  | ||  ||  ||           
TCATGGTTGTTCATATACAGAAGCCCATGATGCACTTGATCCAACTGGCAATATTACAATCAAATGGGATGTCATAAGCTGGACTCCAGACGGCTATATTgtaagtgatcataactttcttaatgtgagaaagacattatattgtgagttttgacatttaacctgaaaagcattttgtagtaagaaataagagctatgta

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G32130.1 (Glycine max), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagt--tcaagaa---cctgaagtaga--aaatattaggccttgtttaccggtttttgattcatctaaactgtttgtttgttcgatctag--------
|||| |||||| |||||||||||   || || || ||||| ||||||||||| || |||||||| || ||||||||||||||||||   ||  ||   | | | ||  |  || || |      ||      |  ||   |   || ||     |   |  |  | || ||         
AAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTTgtaagtgaccacaaatttcttaatgtgcatcaagtactcaaatatgacatgtgccttggaaaatatttatggaatcaataagaactatgtaagactatac

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G35400.1 (Glycine max), 5'ss of exon 1
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagt------------tcaagaac-----ctgaagtagaaaatattaggccttgtttaccggtt---tttgattcatctaaac-tgtttg---tttgttcgatctag---
|||| |||||| | ||||||||| | || || || ||||| ||||||||| |||| |||||||| |||||||||||||||| ||||            ||||   |      | || |   ||  |      ||  |||     ||     ||||   ||||||  | ||||    || |||  ||||    
AAGCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTTGCAAgtctattctttttttcaatgtcgcctattaaaatcagaagcaaataatctgattttataattaaacatgatggttctaaatgtttttggctctttttctctctactag

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G22410.1 (Glycine max), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccg-----gtttttgattcatctaaactgtttgtttgttcgatctag----------
|||| |||||| | ||||||||    || || || ||||| || |||||||| || ||||||||||| ||||||||||||||||||      |  |    ||  |   |||| |   |   ||        |  || ||    | ||     |   |  |    || ||           
AAGCCTATGATCCACTTGATCCTACCGGAAATATAACAATCAAGTGGGATGTCATTAGCTGGACTCCAGATGGCTATGTTgtaagtgaccacaaatttcttaatatgcattaagtactcaatatgacatgtgccttggaaaattttatggaatcaataagaattatgtaagagtagactt

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA19G04210.1 (Glycine max), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccggtttttgatt--catctaaactgtttgtttgtt--cgatctag-----------
|||| |||||| | ||||||||| | || || || ||||| ||||||||| | || || ||||| |||||||| |||||||||||| |       |  |||   |  |||||     ||          | |||||  ||  |||||    || | ||    | | | |           
AAGCTTATGATCCACTTGATCCATATGGAAATATCACAATCAAATGGGATATCATAAGTTGGACCCCTGATGGTTATGTTgtaagtactttcttttacagtttcacctattaatatctgaagcaaatcatctgatttacaattaaacatgatggtcgtaaatgtttttggctcttttttc

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G50750.1 (Glycine max), 5'ss of exon 2
-AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattag------------gccttgtttaccggtttttgattcat-ctaaactgtttgtttgttcgatctag-
 | || |||||| ||||||| ||| | || || || ||||| ||||||||||||||   |||||| |||||||| ||||| ||||||  |      |  | ||  |  |||||              |||  | | |   ||| |  ||     || |||| ||| |         |   
GATGCTTATGATCCGCTTGACCCAAATGGGAATATAACAATCAAATGGGATGTTATATCCTGGACCCCTGATGGATATGTagtaagtatattcttgtacaatatcacctattaatatgagaaccaaacctcctgtcctattttctcctttgcattacactggttgctcacatatattgtt

upper sequence: AT5G60920.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 5'ss of exon 2
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccggtttttgattcatctaaactgtttgtttgttcgatctag-----------------------------------------------------------------
|||| || ||| ||||||||||||| || || || || || || |||||||| |||||||||||||| ||||| ||||||||||||  || |   | || || ||||||||  |  |    ||  |    ||| |  | |  | |   |||  | | |     |                                                                  
AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagt--aaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagc--atccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTTgtaagttcaagaacctgaagtagaaaatattaggccttgtttaccggtttttgattcatctaaactgtttgtttgttcgatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA