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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G52360.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
gtaattcattagtagtcacttgagagtttggaaaatcaaattt--atgcacctttggttaa--ctgtgtgacaa-tattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
    | |||    |  |  ||    |||  |||   |  |||    |  | | ||  | ||  ||      ||  ||| | ||   ||| || || ||||| ||||||||  | |||||||| || |||||||| |||||||||||||||||||||||  | ||||| || || ||||| || 
---gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
gtaattcattagtagtcacttgagagtttggaaaatcaaattt--atgcacctttggttaa--ctgtgtgacaa-tattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG------
    | |||    |  |  ||    |||  |||   |  |||    |  | | ||  | ||  ||      ||  ||| | ||   ||| || || ||||| ||||||||  | |||||||| || |||||||| |||||||||||||||||||||||  | ||||| || || ||||| ||       
---gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 21
---gtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaat--attttttcct---cagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
   |   |     | |     | |       |    | | | || | || | |     ||   ||| |||||||   |  ||| ||   |||||| || || |||||||| || |||||||||||||| || ||||| |||||||||||||| || ||  |  | ||||  || || |||   |||
gtaggcttctgcaattgaatgcatcttgccctactcagtaacatct-tgtatcggacattgtatgt-tgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T02 (Zea mays), 3'ss of exon 20
gtaattcattagtagtcacttgagagtttggaaaatcaaatttat------gcacctttggtta---actgtgtgacaatattttttcct--------cagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
 |  || ||  |||| |   ||  | |      |        ||        || |||   |     | ||| ||   | | ||  ||||        |||||| || || |||||||| || |||||||||||||| || ||||| |||||||||||||| || ||  |  | ||||  || || |||   |||
-tggttgataggtaggcttctgcaattgaatgcatcttgccctactcagtaacatcttgtatcggacattgtatgttgacaattggtcctttgctgtacagTAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
------------------------------------gtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
                                     || |  |  |  ||  |   | | |   ||    | |     |||||  ||    || ||| ||     |||  |||   ||| || ||||| ||||| |||||| | ||||| ||||| ||||| || ||||| || || |||||||| ||  ||||||| ||||||||||| |||
gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagt-----tatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
----------------gtaattcattagtagtcacttgagagtttggaaaatcaaa-------tttatgcacctttggttaactgt-gtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
                || ||   ||| || | || | |  ||   || |   |||       || ||     |   |||   ||| |      |||  |||   ||| || ||||| ||||| |||||| | ||||| ||||| ||||| || ||||| || || |||||||| ||  ||||||| ||||||||||| |||
gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
-------------------------------------------------------------------gtaattcatt-agtagtcact----tgagagtttggaaaatcaaatttatgcacctttggttaactgtgtga----caatattttttcct-cagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
                                                                    || |||||| |  || || |    ||  |||||  |  | | |     |  |  ||  ||| ||||  |        ||||  | |  | |||||| |||||||| ||||||||| | ||||||||||| || ||||| ||||| ||| | |||||| |  |  ||||||| || || |||| ||||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
gtaatt-----cattagtagtcacttgagagtttggaaaatca---aatttatgcacctttggttaactgtgtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
||||||       ||| |    || || ||     || | |     |  |  | ||| |||||   |   |     |  ||| | |   ||| || ||||| || || |||||| |||||||||| || |||||||| ||||| || || |||||||| ||||| ||||||||||| || |  |||
gtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgg--gatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG
                        ggttaac  putative branch site (score: 3)
                                         tattttttcctc  putative PPT
                                   tgacaatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG