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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatattgaatatcacgtcttttcgtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT

Basic information

species Arabidopsis thaliana
transcript AT1G62850.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 5
gtaatatattgaatatcacgtcttttcgtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
                 | |  | |||      || |  ||   |    ||| | |    |  ||  |    |||       |||||||||| || |||||||| || ||||||||||| || || ||| ||||||| |||||||| || || | |||  |
---------------gtatgcttcttcaattcagtttcattttctagggctagaccacttacattactccacaatttgcc--ctgaacagGCAATCATTGATGCTGCATCATATGTTCCTCCACCCCCAACAGAAGACCAAAAGAAAAAGATTGAAAAAAT

upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G14410.1 (Glycine max), 3'ss of exon 5
----gtaatatattgaat---atcacgtcttttc--gtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatca-cataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
       ||| ||||| |    | || |||||||  ||          |   || ||  ||  |  |     ||| |||||| | |     |   || |||  || ||||||||||| || |||||||| || || || |||||||| |||||||||||||| |  ||| |
caacaacataaattgagttcatttacctcttttcttgtttctaaaaactggcttttacttagcaatggtgcttttctgtttatttaatggcaaaaaatagGAAATCATTGATGCGGCATCTTATGTTCCGCCGCCTCCCTCAGAAGAGCAAAAGAAGAAAATTGCGAAGAT

upper sequence: AT1G62850.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 3'ss of exon 6
-------gtaatat-attgaatatcacgtcttttcgtcatggtgtgtt--tcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
        |  | | | |   | |    | |||| |   || ||| ||  | |   ||  |  |     ||| ||    | |  | |   ||   ||||||| || |||||||| ||||||||||| ||||| || ||||||||||| || ||||| ||||| |  ||| |
tgtcattattgtgtgacttgctgttgattatttttgaagtgatgttttgttgagattaattttattattgattttccattattttgaatgaataaaacagGCAATTATTGATGCTGCTTCATATGTCCCACCGCCCCCATCAGAAGAGCAGAAGAAAAAAATTGCCAAGTT

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|86079506|gb|DR375263.1|DR375263
EST:     AGGCAACATCGACGATGCACTTGAAAAACTACAG                         GCGATCATTGATGCGGCTTCTTATGTTCCACCTCCACCATCAGAAGAACAG
genomic: AGGTAACATCGACGATGCACTTGAAAAACTACAGgtaatatatt ... aactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAA
EST: gi|19741759|gb|AU227112.1|AU227112
EST:     AGGTAACATCGACGATGCACTTGAAAAACTACAG                         GCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAA
genomic: AGGTAACATCGACGATGCACTTGAAAAACTACAGgtaatatatt ... aactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAA
EST: gi|86074747|gb|DR370504.1|DR370504
EST:     AGGCAACATCGACGATGCACTTGAAAAACTACAG                         GCGATCATTGATGCGGCTTCTTATGTTCCACCTCCACCATCAGAAGAACAG
genomic: AGGTAACATCGACGATGCACTTGAAAAACTACAGgtaatatatt ... aactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT
                                         acataac  putative branch site (score: 3)
                         atgtttttgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatattgaatatcacgtcttttcgtcatggtgtgtttcattctatctaaaacggagatgtttttgtttaatcacataactgaacagGCGATAATTGATGCGGCTTCATATGTTCCACCTCCACCATCAGAAGAACAAAAGAAGAAAATAGTAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA