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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT

Basic information

species Arabidopsis thaliana
transcript AT2G20190.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g40430.1 (Oryza sativa), 3'ss of exon 14
------------------gtattgagttt---ctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaat---tgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATC----CAATAGTCACACAAGTAGCGCA-GCTGCTGAATCAACACATAGTAT
                     | ||||||   ||||| ||||| |  |  |  || ||    |   |   |   || |    ||  |   | |     | || |||   | | ||||||| | ||||||||||||||||| |||||||| ||||||||||||||| |||    || |||  | || ||    ||   |||     || |   ||   ||||| ||  |  | |     
gtattctttaagctgcttaattggagtttgctctttcattatgtagtttaaaattcttagctat-tgctttccgacttatattataaatacttaagaaatctcaatttcttttttcttttcctcctagtgcagGAGTTGATCCTCCATCCTCTCGTGATCCTCCTATCCCACTTGCTGCAACTGCTTCGGACCATCTGTCTTTGCAGAATTCCATATTGCTGGATTCATCCCT-----

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 13
----------------------------------------gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgag----ctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTC-----ACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT
                                         ||   |    ||||  | ||| |  | | | |  ||     |   |  | | |  | ||    ||| ||||        ||| |   || | | |||||   ||||||||||| ||||| |||||||||||||||||||||||| | |    ||  ||  |||| || |||  ||       |||     |    |||||  |   |    |     
gtattcttttaactgcttagttgtcaattactgttaagtaatagaaatggccttttatcatgtatttcctggtcattgactgacaatattatcatcttagttttctatgataaaaaaaatcagtttc-ttatttccttttaatcctagtgcagGGGTTGATCCTCCATCGTCTCGTGATCCTCCTGTTCCGCTTGCAGCAACAGCTTCAAATCATCTGTCCTTACAGAATTCAGCACTGCTCGACTCATCTGT-----

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
------gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACA---AGTAGCGCAGC--TGCTGAATCAACACATAGTAT
       |||| | ||  | | | |  |  |  ||| | | |||||      | |  | | |  |   ||| | |  || |         || | | |||||   ||||||||||||||||| |||||||| ||||||||||||||| | |    ||  || |||||||| |||  ||   ||      | | ||||  || || |   |  | |     
ggggcattattaatttattatgcatcagggaacacattctattttt------ttcactgatactataaaagttttaatttc---------ttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT-----

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
------------------------------gtattgagtttctttccttatgaaagtacagtttgtttt-tgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttcttttt-cccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT
                               ||||  ||  ||    ||     | || |  |  ||   ||     ||  |||   |    | | |  |  ||| || | |||||| |  |||| || |||||||||||||||||||||||||||| ||||||||||| ||||||| ||||| ||  || ||||| |||  ||  |||||      | | |    | | ||   | | ||
gtaccacataagttttcctgttagttatttttattt-gtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaac-tatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 13
------------------------gtattgagtttctttcctta--tgaaagtacagtttgtttttgaaacgt----cctttaacatgagctaagatatccttgcgcagctaaattgtcttcttttt-cccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT
                         ||||    || || ||| |  |   || ||    ||   || ||  ||    |  |||   |    | | |  |  ||| || |||||||| |  |||| || |||||||||||||||||||||||||||| ||||||||||| ||||||| ||| | ||  || ||||| |||  ||  |||||      | |  | ||||||||   |     
gtacaacataagttttcctgttatatatttttatttttacctcaattttcaggacttgatgccattcaatggttgatctgttagtgttttttcaaac-tatttgagcggctaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCAGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAACAGAATCAACTACTTCCGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 13
------------------------------gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgt-------cctttaacatgagctaagatatccttgcgcagctaaatt-gtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAAC-ACATAGTAT
                               ||||   | |   || || |    |    |||    ||  | |  |       |   | | |||   |   |  |   || || ||||||||  |||  | || ||||||||||||||||||||||||| || ||||||||||| || |||| ||||| ||   ||||||| |||  ||  || ||      | |  | ||||||||  |||     
gtaccaaataagtttacttgttaaatatatatattttttctacctcattgttctggacttgttgccattcaacaattgatgatgctagtgatatggtttttaaactttgtgagcggctaaatttatctcttattgcccctagtgcagGAGTTGACCCTCCCTCATCTCGTGATCCACCATTCCCTGCTGCTGTCACAGCATCTAATCATCTAACTAGCTCTTTAACGACAGAATCAACTGCATCTGG-

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 13
--------------------------gtattgagtttctttcc-------ttatgaaagta----cagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaatt-gtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT-
                           |||  | ||| | | |       || || |  |     || |      ||||     |   | | |||   |   |  |   || || ||||||||  |||  | || ||||||||||||||||||||||||| || ||||||||||| || |||| ||||| ||   ||||||| |||  ||  || ||      | | || ||||||||    ||    
gtaccaaataagtttacttgttaaatatatatattttttctaccacattgttctggacttgttgccattcaacaattgatgaagctagtgatatggtttttaaactttgtgagcggctaaatttatctcttattgcccctagtgcagGAGTTGACCCTCCCTCATCTCGTGATCCACCATTCCCTGCTGCTGTCACAGCATCTAATCATCTGACTAGCTCTTTAACGGCAGAATCAAC-TGCAGCTGG

upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------------------------------------------------------gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttcttttt-cccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT
                                                                                       | |||| |  || || | ||  |   |  ||        ||| |   ||||||  |    | |   ||   ||  | ||||| || |  |||| || ||||||| |||||||||||||||||||| |||||||||||||| || | |  || || ||||||||| |||   |  ||||  |   |    |  |||||||    |  || 
gtattgaatggttttgtcaattagattattatctttgatcataatattaatttgactgtcaatctatgaagctattcaatggtttactgttgaatcactatc-tgattgaccaatggtcaaaa--cgaagctgtctttaatgt---ttgaacaatttatgaacggctaagtttttctcttattgcccctagcgcagGAGTTGACCCTCCATCATCTCGTGATCCTCCATTTCCTCTTGCTGTTCCAGCATCAAATCAACTTACAAACACTTCGATGGTAGAATCAAATGCTTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgagctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT
                       agctaaa  putative branch site (score: 3)
                              ttgtcttctttttccc  CT-rich tract
       taagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACAAGTAGCGCAGCTGCTGAATCAACACATAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT