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'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG

Basic information

species Arabidopsis thaliana
transcript AT5G20000.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 5
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                                        ||   |     | |  | |  |||  | |   ||  |      | ||| ||  ||   | |    | ||         ||| | || |  ||        | | |  ||||||| || ||||||||||||||||| || ||||| |||||||| ||||||||||| || |||||||||||||||||||||||||||||||| || || || |
------------------------------------------------------------------------gtaagtggcaatcacttcttttttttttctgcaagcagcagagttcatgctacttcatctcgtcatcagttc------tttagttacttaatcgcatctttttctcctgcagTCCCGCTTTGATATCTTGAAGATTCATTCAAGAAAAATGAACTTGATGCGTGGCATTGATCTGAAAAAGATTGCAGAGAAGATGAATGGGGCATCTGGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                                        ||   |  || |||  ||   | || ||  |    || ||||  |   | || ||||                || | |  |  ||   | |  ||             |||||||| ||||||||||||||||| || ||||| |||||||| ||||||||||| || |||||||||||||| || || ||||||||||| |||||||| |
------------------------------------------------------------------------gtaagtgctgataacttactgtatattgtttgtgttaatttttccatgatttcttgtgtt-------------gatgatgcgcttatcttttgcttt------------cagTCACGCTTTGATATCTTGAAGATTCATTCAAGAAAAATGAACTTGATGCGTGGTATTGATCTGAAAAAGATCGCTGAAAAGATGAATGGGGCTTCAGGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                                                             | |  |  |  || |  |  | |  ||||   |||  |  |   |  |||    |    || | |  ||   |  |   | |    ||||||||||||| |||||  ||||||| || |||||||||||||| ||||||||||| ||||||||||||||||| ||||| ||||||||||| || ||||| |
--------------------------------------------------------------------------------------------gtatgttcggctaactcatcctgtt-ataccagttgatctta---tatggctactcctgctgac-agggtgcttaacctttttcccctgcagTCACGTTTCGATATTCTGAAGATCCATTCAAGGAAAATGAACTTGATGCGTGGTATCGATCTGAAAAAGATCGCAGAAAAGATGAATGGGGCCTCAGGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                                                             | |  |  |  || |  |  | |  |||| | ||| |    |  || |  |   | | |        |  || |  |  |     |||||||||||||| |||||||||||||| || ||||| |||||||| ||||||||||| || |||||||||||||| || || ||||||||||| || ||||| |
--------------------------------------------------------------------------------------------gtatgtttggctaactcatcctgtt-atacctgttg-attttacatg-gctactgctgctgacagggcgcttaatctt--ttgcccttgcagTCACGTTTCGATATCTTGAAGATCCATTCAAGAAAAATGAACTTGATGCGTGGCATTGATCTGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                     | |||  ||||||   | | |  |  ||  |||  |||  | ||||| |  ||| |  |        || |  || |  |  |   | | |      |   |  ||||  ||||| |      |  ||||||| ||  | ||||| ||||| || || ||||| | ||||||||| |||||||| || |||||||| |||||||| |||||||||||||| || || ||||
---------------------------------------------------gtttgcatttttgct---ttcatgctacttattaatatatt-tgtactgggagaaaaagat------gcacctggtgcattcctaaaaaagtat-----tcctgaaaatggctatttat------ttatgcagTCTCGGCTGGATATTTTGAAAATCCATTCAAGAAGAATGAATTTAATGCGTGGCATTGATCTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                     | |||  ||||||   | | |  |      |||  |||  | ||||| |  |||   |         || |  || |  || |   |   |      |   |  ||||  ||||| | ||       |||||| ||  | ||||| ||||| || || || || | ||||||||| |||||||| || ||| |||| |||||||| |||||||||||||| || || ||||
---------------------------------------------------gtttgcatttttgct---ttcatgctacccattaatatatt-tgtactgggagaaaagat-------gcacctggtgcattcataaaaaaatat-----tcctgaaaatgagtattttttat-------gcagTCTCGGCTGGATATTTTGAAAATCCATTCTAGAAGAATGAATTTAATGCGTGGCATTGATTTGAAGAAGATTGCCGAGAAGATGAATGGAGCATCTGGTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgc--agTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                                                        |||  |||   |  ||    | ||  ||   |  |   | |      |        | |  |  |   | |   || ||| |  | ||  || |  |||| || |  ||||| || || |||||||| ||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| || ||||
--------------------------------------------------------------------------------------gttatggtttttaggatatgtgatttgactttctggtagctatgttgctatctgactggcattgcatatattaaagatttttattttttgaattactcagTCTCGCTGGGATATTTTAAAAATACACTCGAGGAAAATGAATTTGATGCGTGGGATCGATCTGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTG

upper sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 7
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                                                        ||| |  ||   ||      ||| | |  | | |   | ||| |   ||   | || |   || |||| |||          ||| || | | ||| |    | | || ||||| || |||||||| ||||| || |||||||| |||||||| || |||||||| || |||||||| ||||| |||||||||||||||||||| || ||||
-----------------------------------------------------------------------agttatgattataaattcgatattcattctg-atatggcatttttttttatcaactgca---aaggtgaagcacat-------gctgattttttttttt--cttttttttcagTCCCGCTTTGATATTTTGAAAATCCACTCAAGAAAAATGAACTTAATGCGTGGGATTGATCTGAAGAAGATAGCAGAGAAGATGAATGGTGCATCTGGTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116400365|gb|EG442957.1|EG442957
EST:     GGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG                         TCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGT
genomic: GGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAGgtaatgcttg ... tgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGT
EST: gi|86079899|gb|DR375656.1|DR375656
EST:     GGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAG                         TCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGT
genomic: GGCCTGGAAGGATTGATAGGAAAATTGAATTTCCTAATCCTAATGAAGAGgtaatgcttg ... tgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG
                                     ttctaat  putative branch site (score: 2)
                           taatgtatatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcttgtgtttcttaggacatgatattagaaataactttaaacttgaagtagcaactttgctcactccgttgtttttggtaaactatcatttactgcgtaaaatacttttctccatacttattgtacccaaagtgaggcaggacggtttggctaatgtatatttctaatatgtgttgcagTCACGTTTTGATATCTTGAAGATACACTCAAGGAAAATGAATTTGATGCGTGGAATCGATCTGAAAAAGATTGCAGAGAAGATGAATGGTGCTTCAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG