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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaattttttttatgtgttacttccaatacaattgtgtagttattgtgattaatatactaagttcaatctaatggactctaaactcattttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGTTGTTTGCAAGAACACTCTCTGCAATAAAGTCTCAGCAATGTGAAATTTC

Basic information

species Arabidopsis thaliana
transcript AT2G31490.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G31490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0055g00700.t01 (Vitis vinifera), 3'ss of exon 1
-tggaaattttttttatgtgttacttccaatacaattgtgtagttattgtgattaatatactaagttcaatctaatggactctaaactcattttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGTTGTTTGCAAGAACACTCTCTGCAATAAAGTCTCAGCAATGTGAAATTTC--
 ||||      | |   || ||  || ||||  | || ||   ||||  | ||  | ||| |  ||| | |       | |||  |  | | |  ||| |||||||||||||||| ||||| || || |||||||| |||||||| ||||  |||||   |   |  |      |||   |  |    ||  |  | || |  
ttggatgcaactatgtagtatttttttcaattaatttctgagattatattaatacaaatattgtgttaatttcttcatattctggaa-cttgtggtgacagCATATGCAAGATGAGGATGCTGGGAGGCCACACAGGAAGTTCCTATGAG--TGTTTTGCAATTCGTTTGTAATAATGGTGGATGGAAAAACTAGATTTCCTC
















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|164150465|gb|ES196568.1|ES196568
EST:     TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAGTCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACACAGAA
genomic: TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAA
EST: gi|164217748|gb|ES085790.1|ES085790
EST:     CTACAAGGGAATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGAT
genomic: CTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
EST: gi|125271671|gb|EL285756.1|EL285756
EST:     TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACA
genomic: TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACA
EST: gi|164038600|gb|ES101661.1|ES101661
EST:     TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCA
genomic: TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCA
EST: gi|125253753|gb|EL267838.1|EL267838
EST:     AATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
genomic: AATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
EST: gi|116470379|gb|EG512971.1|EG512971
EST:     TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
genomic: TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
EST: gi|19799339|gb|AU230629.1|AU230629
EST:     TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
genomic: TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
EST: gi|47829331|gb|CK119015.1|CK119015
EST:     TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTC                         CATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT
genomic: TCGGCATCGCTCTCCCGATCATTGTCTACAAGGGAATCGTCAAAGATTTCgtgagtttaa ... tttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgattaatatactaagttcaatctaatggactctaaactcattttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGTTGTTTGCAAGAACACTCTCTGCAATAAAGTCTCAGCAATGTGAAATTTC
                                 ctctaaa  putative branch site (score: 3)
                                        ctcatttttt  CT-rich tract
     attaatatactaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaaattttttttatgtgttacttccaatacaattgtgtagttattgtgattaatatactaagttcaatctaatggactctaaactcattttttgatagCATATGCAAGATGAAGATGCAGGCAGACCACACAGAAAGTTCCTCTGAGGTTGTTTGCAAGAACACTCTCTGCAATAAAGTCTCAGCAATGTGAAATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - caataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactca