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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctttctctcttctcctttgatttcaatatttgtcaatgccttgctttgtaacttctaaatctgggatttgtatagaagctatggttattgtgaatctcgatctatgtgtatggatccgaaaatctaaggatgttaattttttggttattgttagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAATTCACTTGTTCAAAGCTGGTGTTGAGCCAAAGTGGGAAGATCCAGAGTGT

Basic information

species Arabidopsis thaliana
transcript AT5G35620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 1
gttcgtctttctctcttctcctttgatttcaatatttgtcaatgccttgctttgtaacttctaaatctgggatttgtatagaagctatggttattgtgaatctcgatctatgtgtatggatccgaaaatctaaggatgttaatttt-ttggttattgtt--agATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAATTCACTTGTTCAAAGCTGGTGTTGAGCCAAAGTGGGAAGATCCAGAGTGT
                                                         || |  | | | ||||   | |  |   | || || |  |     |    |||| |||   |    ||   ||     || | |||    ||  || ||| |  || ||| | ||    || || |   | |||||  ||||||  ||||||||  |||| || ||||| |||||||| || |||||||||||||| |||||||||
--------------------------------------------------------cctgcctattatcggatacttttgaa---tttgattgtcct----tttatcctatatgtgcaggcatgatcttcctttcatttaaatccccttatttcttgctgcagCTTGTATGATCAGATTTTCCGTCCAAGCAAGGTGACAGTAAATGCTGATTTTCATTTATTCAAGGCTGGTGTAGAACCAAAGTGGGAAGACCCAGAGTGT

upper sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0049g01770.t01 (Vitis vinifera), 3'ss of exon 1
gttcgtctttctctcttctcctttgatttcaatatttgtcaatgccttgctttgtaacttctaaatctgggatttgtatagaagctatggttattgtgaatctcgatctatgtgtatggatccgaaaatctaaggatgttaattttttggttattgt-tagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAATTCACTTGTTCAAAGCTGGTGTTGAGCCAAAGTGGGAAGATCCAGAGTGT
                                                   |||   ||| |  ||      ||| |||  |   |||   | || | ||||  |||  || | | |   | |  | |  ||  ||    ||  |    ||  ||||  ||  || | ||    |||||| || | ||||| ||| |||| ||||| ||  | || |||||||||||||| ||||| ||||| ||||||||||| ||||||
--------------------------------------------------attgattcttttgtattct---tttttatcaa---tatcagttttttaaatca-gattcatttatgtaccttcttacacatattga----aaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT
















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|164157706|gb|ES174946.1|ES174946
EST:     GCTTCTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGG                         ATTGCACGAGACTA
genomic: GCTTCTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGGgttcgtcttt ... ttattgttagATTGCACGAGACTA
EST: gi|124725523|gb|EH816925.1|EH816925
EST:     GCTTCTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGG                         ATTGCACGAGACTATATTTC
genomic: GCTTCTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGGgttcgtcttt ... ttattgttagATTGCACGAGACTATATTTC
EST: gi|125101753|gb|EL156767.1|EL156767
EST:     TACTTTCGACACCGTCGAAGATTTTTGGGG                         ATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAAT
genomic: TACTTTCGACACCGTCGAAGATTTTTGGGGgttcgtcttt ... ttattgttagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAAT
EST: gi|116473054|gb|EG515646.1|EG515646
EST:     GCTTCTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGG                         ATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAAT
genomic: GCTTCTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGGgttcgtcttt ... ttattgttagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAAT
EST: gi|124839286|gb|EH923725.1|EH923725
EST:     CTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGG                         ATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAAT
genomic: CTCTTCGTAAAGCCTATACTTTCGACACCGTCGAAGATTTTTGGGGgttcgtcttt ... ttattgttagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatgtgtatggatccgaaaatctaaggatgttaattttttggttattgttagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAATTCACTTGTTCAAAGCTGGTGTTGAGCCAAAGTGGGAAGATCCAGAGTGT
                               tgttaat  putative branch site (score: 3)
                                 ttaattttttggttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtctttctctcttctcctttgatttcaatatttgtcaatgccttgctttgtaacttctaaatctgggatttgtatagaagctatggttattgtgaatctcgatctatgtgtatggatccgaaaatctaaggatgttaattttttggttattgttagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAATTCACTTGTTCAAAGCTGGTGTTGAGCCAAAGTGGGAAGATCCAGAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA