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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttcactgttgctaagtattaacctttcattactgtatgtagtagcgtcttttggcttttccccccttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG

Basic information

species Arabidopsis thaliana
transcript AT4G35260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 2
------------acttcactgttgctaagtattaacctttcattactgtatgtagtagcgtcttttggcttttccccccttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG
             ||| | |||  |  ||| || |  |    ||  | |   ||     |   ||| | |||  |   || || |        ||| ||      |||| |||| ||||| ||||| ||||| ||| | || || ||||| ||||| ||||||||||||||||| || |||||||||||||
tgaaggatgttttcttgattgtcacagagttttcagatcaagtttgtttgattaactaggaacttttgatttagcatgctcttgt--------tttgtgtg----tttgtagGTCACGCCAAATCTTTATGGCAATCTGGTGGCTAACACGGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 2
acttcactgttgctaagtattaacctttcattactgtatgtagta-gcgtcttttggcttttccccc----cttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG
    |||| || || | || |    || |   |   |   |  || |  ||     |   ||||  |     || ||       | | | ||  | |||||| |||| || || || || ||||| ||||| ||||| ||||| ||||| |||||||||||||| ||||| || ||||||||||
----cact-ttcctgaatactggttttcccaaatgattcctgttaagtatccccgtgtaattcctgcagaatttctaactttctactctttggtacgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 2
acttcactgttgctaagtattaacctttcattactgtatgtagtagcgtcttttggct-tttccccccttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG
  |  |  |    |   |   |   |   || |   | |  | |    |  || |  |   |      ||| |  | |    | | ||     ||||| |||| || || ||||| ||||| ||| | || || ||    ||||| ||||||||||||||||| || |||||||||||||
-ttctaaagggctttttttccagaataatatgaagatttcaaatgatttaattagattacctgtggagtttgaacatacttttctttggttccttttgtagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 2
acttcactgttgctaagtattaacctttcattactgtatgtagtagcgtcttttggcttttccccccttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG
 | ||||  ||  |   |  |  |||    ||   | |||       |    |   |  |         ||||    |   || |     | ||||| |||| ||||| ||||| ||||| ||||| || || ||||| ||||| ||||||| |||||| || ||  ||||||||||||
tcatcacatttcttttctgctttcctaattttctcgaatgcttctttgcaaatacaccatggattaggattatctgtgggtttcaatcttttttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATTGTTGGAGGGACGGGCATCATGCCTGGAG

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|125091556|gb|EL149379.1|EL149379
EST:     CTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTAT
genomic: CTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTAT
EST: gi|125068361|gb|EL134534.1|EL134534
EST:     CAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATT
genomic: CAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATT
EST: gi|124819303|gb|EH904169.1|EH904169
EST:     CAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATT
genomic: CAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATT
EST: gi|124797348|gb|EH887027.1|EH887027
EST:     ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGG
genomic: ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGG
EST: gi|124897399|gb|EH973613.1|EH973613
EST:     ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGGAATTTAGTTG
genomic: ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTG
EST: gi|125306588|gb|EL320673.1|EL320673
EST:     CAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATT
genomic: CAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATT
EST: gi|164057705|gb|ES074810.1|ES074810
EST:     ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATCTCTATGGGAA
genomic: ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATCTCTATGGGAA
EST: gi|125126901|gb|EL171968.1|EL171968
EST:     ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATG                         GTAACGCCGAATC
genomic: ATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttca ... tgttttgcagGTAACGCCGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtcttttggcttttccccccttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG
                        ttataac  putative branch site (score: 2)
                                  aatttatgaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttcactgttgctaagtattaacctttcattactgtatgtagtagcgtcttttggcttttccccccttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acagcaa