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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaacaatcatgattttcacgtttttggtttgtttatatgattttcaccttccattgcataactcatcataatcccctttgaaataaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G44350.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 5
gtagaaacaatcatgattttcac-gtttttggtttgtttat--atgattttcaccttccattg-cataactcatcataatcccctttgaaataaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
      |   |  || | || |   ||| ||| |||||| |  | | | | |    |  ||||   |||    | | |||    |||  |   |||||  ||||||| |||||||||||||||||| ||||||||||||| ||||||||||||||||| |||
----gtatgcttttggtattgattatttatggattgtttctcaagggtgtcctttattgattggtctaaaatctta-aatggtgttt--atccaagGTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 4
gtagaaacaatcatgattttcacgtttttggtttgtttatatgattttcaccttccattg-----cataactcatcataatcccctttgaaataa---------agGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
      |  ||  || | |  |   |||  |  |   | |||   | |  | ||  |  |     | ||| | ||     |    | |  |||           ||||  |||| || |||||||| |||| |||| ||||||||||||| ||||||||||||||||| |||
----gtatgattctgctatcgattatttatggataaatctattgctattgctttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 5
gtagaaacaatcatgattttcacgtttttggtttgtttatatgatttt-caccttccattg-cataactcatcataatcccctttgaaataa----agGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
|||  |   ||      |     || | ||| | ||||   || ||||  | | |  | |  | || |     | | |||    |||  |      ||||  |||||||||||||||||||||||||| ||||||||||||| ||  | ||||| || || |||
gtatgatatattgcttatcaattgtctatggatagttttgttgcttttatagcatatactaacttatcctgggaaattcctgaatgatgttcctccagGTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 5
gtagaaacaatcatgattttcacgtttttggtttgtttatatgattttcaccttccattgcataactcatcat-----aatcccctttgaaat----aaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
||| ||   |       ||    |  | ||| | ||| || |   |||       |||    |||||||||||     |||||    | |  |      ||||  ||||||||||||||||||||| |||| ||||||||||||| ||  | |||||||| || |||
gtataatatactgcttattagttgcctatggatagtt-atgttgcttttctagagcatatattaactcatcatgtgaaaatccttaataatgttcctgcagGTCCTTGGTGGAATGAGAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 4
gtagaaacaatcatgattttcacgtttttggtttgtttatatgattttcaccttccattgcataactcatcataatcccctttgaaataaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
||| ||   ||  || || |||  ||     | | | ||||   || || | || | | | ||||        |||    ||     |  ||||  ||||||||||||||||||| | |||| |||||||||| || ||  |  | ||||| || |||
gtataat--atactgcttatca-attgcctatatatgtatagctttgtcgcttttc-taggataatgttcttgaataatgttcc---tgcagGTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAG

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 5
gtagaaacaatcatgattt-tcacgtttttggtttgtttatatgatt-------------ttcaccttccattgcataactcatca-----taatcccctttgaaat---aaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
|||   | | ||    ||| |   | | || ||  ||||| |   ||                |  || || ||  ||||   |||     | ||| |  |   |||   ||||||  |||||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| || || 
gtaatgatagtctctgtttattctgatgtttgtaagtttacaatcttagagcaacacgtacatatattacagtgtgtaacctctcactgagttatcactgtcacaattgcaaagGTACTTGGTGGAATGAGAGGAATGACAGGGTTGCTGTGGGAAACCTCGTTGCTTGACCCAGATGAA

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|124981386|gb|EL054258.1|EL054258
EST:     GAAGTCAGAACTATGGGAAGGTCCAACTGGGAAACATCACTGTTGATATG                         GTTATTGGTGGAATGAGAGGGATGACTG
genomic: GAAGTCAGAAC-ATGGGAAGGTCCAACTGGGAAACATCACTGTTGATATGgtagaaacaa ... tgaaataaagGTTATTGGTGGAATGAGAGGGATGACTG
EST: gi|164102586|gb|ES032213.1|ES032213
EST:     TGAAGTCAGAACATGGGAAGGTCCAACTGGGAAACATCACTGTTGATATG                         GTTATTGGTGGAA
genomic: TGAAGTCAGAACATGGGAAGGTCCAACTGGGAAACATCACTGTTGATATGgtagaaacaa ... tgaaataaagGTTATTGGTGGAA
EST: gi|47832067|gb|CK121751.1|CK121751
EST:     TGAAGTCAGAACATGGGAAGGTCCAACTGGGAAACATCACTGTTGATATG                         GTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTG
genomic: TGAAGTCAGAACATGGGAAGGTCCAACTGGGAAACATCACTGTTGATATGgtagaaacaa ... tgaaataaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgattttcaccttccattgcataactcatcataatcccctttgaaataaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG
                      gcataac  putative branch site (score: 3)
                                      tccccttt  putative PPT
                                           tttgaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaacaatcatgattttcacgtttttggtttgtttatatgattttcaccttccattgcataactcatcataatcccctttgaaataaagGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA