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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggacaacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG

Basic information

species Arabidopsis thaliana
transcript AT5G40200.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 2
-----gttggacaacacatttgacat----gatatttttccttatctgactagggagttaagggcacttataaaaatgttttctgtttttgtctttt---cagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
      ||   |  |||| ||  |||     ||| | ||   | |  |  ||    ||| ||   | | ||||   | ||  || ||   || || |   ||||| |||||||||||||| || || ||||| ||||| || || |||||||| |  || |||||||||||||| || ||||| ||| | ||||| |||||||
gttcattttctccccacaattctcatttagaatagtattatctgtgaggataacatgttgaga--aatcataagtcttttaacttttggggttttatggacagATAGATGCAGCTATTAACTCAGGAAATTCAGGTGGCCCAGCTTTTAATGACAGGGGCAAATGTGTTGGTATAGCTTTTCAATCTCTCAAACATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------gttggacaacacatttgacatgatattt-ttccttatctgactagggagttaagggcactta---taaaaatgt-tttctgtttttgtcttttca-------gATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
                                         ||   ||  |   | |||||  | |||  | ||  |  || |      | |    | ||||   |   |   |  ||  |||||     |||||       ||| ||||||||||| ||||| || || ||||| || ||||| ||||||||||| || || ||||| || || || ||||| ||| | |||||||||||||
gtttttctcttaagatctttgcatgcttttgattgtctatattttgca-tattgtagacatagtttttacttctctttggaattatttctaataatctcttaacctgggagcatacttaagttttcactgtttcatggaacagATAGATGCAGCTATAAATTCAGGAAACTCTGGGGGCCCTGCTTTTAATGATAAGGGCAAGTGTGTGGGCATAGCTTTTCAATCTCTTAAACACGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G144501_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------gttggacaacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaatgtttt---ctgtttttgtctttt---cagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
                                               |        |  ||  |  |||  |   ||  |     | ||   | |||   ||  |||     |||| |    | |   ||||||| |    |||| ||||||||||||||||| || ||||| |||||||| || |||||||||| ||| |||||||| ||||| |||||||| ||| | ||||| |||||||
gtacctttcccccctgaaattataataacttcaaataaacctttatataaagatggatgttgcaagtgaagtaaatctattgagaaataataacttatctgc--ttaccggcatgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGTCCAGCTTTTAATGATAGAGGCAAATGTGTCGGTATAGCATTTCAATCTCTTAAACATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------gttggacaacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
                                              |      | |  ||  |  |||  |   |  ||     | |   || |||  ||| |    |    | |  |   || |  | ||   |||| ||||||||||||||||| || ||||| ||||| || || ||||||||||  ||||||||||| ||||| || ||||||||| | ||||| |||||||
gtacatttttttctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
----------------------------------------------------gttggacaacacatttgacatga-tatttttccttatc-tgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
                                                    | | ||     ||  |||  | | ||||||     | | |||||     | | |  |   |    || | |     ||| ||    ||   |||| ||||||||||||||||| || ||||| ||||| || || ||||||||||  ||||||||||| ||||| || ||||||||| | ||||| |||||||
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttg---ttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G015959_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------gttggacaacacatttgacatga-tatttttccttatc-tgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
                                                   | | ||     ||  |||  | | ||||||     ||| |||||     | | |  |   |    || | |     ||| ||    ||   |||| ||||||||||||||||| || ||||| ||||| ||  | ||||||||||  ||||||||||| ||||| || ||||||||| | ||||| |||||||
gtacattttttctctaaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaatacgggccttgtcttg---ttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAACTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 3
---------------gttgga--caacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaa----tgttttctgtttttgtctttt---cagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
                ||  |  |  || | ||    | |||  ||| | | |   ||   | | |      |||||||  |||    |||| ||||||| |  ||  |   ||||| ||||||||||| ||||| || ||||| || || ||||| || |||||||| ||||||||||||||||| || || || ||| | ||||| |||||||
gtattaacgtattgtattatattctgcatacttttacttatagatttgccttttatacgttgaactatgccacacttatgtaaacttctgttgtctgtttattactcataaacagATAGATGCAGCTATAAATTCAGGAAATTCAGGGGGGCCTGCTTTCAATGATAAGGGAAAATGTGTTGGTATAGCTTTCCAATCTCTTAAACATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G09970.1 (Glycine max), 3'ss of exon 2
-gttggacaacacatttgacatgatatt-tttcctta--tctgactagggagttaagggcacttataaaaatgttttctgttt----ttgtctttt-cagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
  ||   |   | |    | ||   ||| |  |||||  | ||| |      ||      |  |||   ||| ||   |  ||    ||||||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| |||||||| ||||| || ||||||||||||||  | || || |||||||
aattaagctgtatacccaaaatccaattgtacccttagttatgaatgcatgatttgtttaatgtatcctaattttccttcattaaggttgtcttttgcagATTGATGCTGCTATAAACTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G01930.1 (Glycine max), 3'ss of exon 2
gttggacaa--cacatttgacatg-atatttttccttatct---gactaggga---gttaagggcacttataaaaatgttttctgtttttgtctttt-cagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
 ||    ||   | |    | ||  | || || |||||  |    |||   ||   ||| |  | |     |      ||   |    ||||||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||||||||| |||||||| ||||| || ||||||||||||||  | || || |||||||
-ttaattaaggtatagccaaaatccaaatgttcccttagttatgaacttatgatttgtttaatgtatcctgattttccttcattaaggttgtcttttgcagATAGATGCTGCTATAAATTCTGGCAATTCTGGTGGACCTGCATTTAATGACAAAGGAAACTGTGTGGGGATTGCATTTCAGTCCCTCAAGCATGAAGATG

upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 2
gttg-gacaacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaatgttttctgtttttgtc---ttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
||   |    |||||||  | |  | || |   |||  |      ||  |   |  |  || |    |||| | || || |||     ||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| || ||||| || || || ||||| || ||||||||||||||| | ||||| |||||||
gtcatggggtcacatttctcct--ttttctcttttagttattgttggcttgttgatccatttttctgatgtctcctattcttgatggttttacagATAGATGCTGCTATAAACTCTGGAAATTCTGGTGGGCCTGCCTTCAATGAGAAGGGCAATTGTGTGGGCATTGCATTTCAGTCTCTTAAACATGAAGATG

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|124857504|gb|EH941941.1|EH941941
EST:     CTTTTGGGATTGCAG                         ATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGAT
genomic: CTTTTGGGATTGCAGgttggacaac ... gtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
 atctgac  putative branch site (score: 3)
                               tgttttctgtttttgt  putative PPT
                      ttataaaaatgttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggacaacacatttgacatgatatttttccttatctgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG