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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatgatctttcatattattgtaaatgttaattctgcataacactagtttgttgaatctaggtgatgaatgcacatgctatagagatcaatgccctcaatgattaatccatctatggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTCACAGGAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 4
gtttatgatctttcatattattgtaaatgttaattctgcataacactagtttg----ttgaatctaggtgatgaatgcacatgctatagagatcaat-gccctcaatgattaatccatctatggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTCACAGGAGAG
  |||| || |||| |||| || | ||| |   || ||| | | | |   ||     ||| || ||    ||||  |  |    |||  ||| || |  |  |  || | | |   |  |  |  |||||||| |||||||| || || || || |||||||| | |||||| ||||| ||||||||||||
-gttatcatttttc-tatttttatgaatatcttttttgcttgagattgtattcagatttgcatttaccctatgatagttc-cattatccagagcacttacgttttattactgacttactt--gattttcagGTCTTTGAAGGCACTTCAGGAATAGACAACAAATATACCACTGTGCAGTTCACAGGAGAG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 4
gtttatgatctttcatattattgtaaatgttaattctgcataacactagtttgttgaatctaggtgatgaat-gcacatgctatagagatcaatgcc-ctcaatgattaatccatctatggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTCACAGGAGAG
                           || ||   ||    |    || | | | ||   ||  |  | ||| | | ||  | |     | | |    ||  || |||      | ||       |||||||||||||| || ||||| ||||||||||| |  || ||||||||||| || || |||
--------------------------ctgcta--ccttttaagttttaatctttagatggtatatagttaatagtatataatttctctcttattttagcttgatcattttctgttttaatttccccagGTTTTTGAAGGCACTTCTGGAATTGACAACAAATACACAACCGTGCAATTTACTGGGGAG
















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|116471926|gb|EG514518.1|EG514518
EST:     CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG                         GTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
genomic: CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
EST: gi|164205189|gb|ES189234.1|ES189234
EST:     ATGGGGAGAAAGCTGTTGTCCAG                         GTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
genomic: ATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
EST: gi|125199027|gb|EL213981.1|EL213981
EST:     ACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG                         GTTTTTGAAGGAACATCTGGGATTGACA
genomic: ACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACA
EST: gi|116483049|gb|EG525641.1|EG525641
EST:     CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG                         GTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
genomic: CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
EST: gi|116424900|gb|EG467492.1|EG467492
EST:     CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG                         GTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
genomic: CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
EST: gi|152038085|gb|BP807684.2|BP807684
EST:     CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG                         GTTTTGGAAGGAACATCTGGGATTGACAACAAGTTCACCACCGTGCAATTC
genomic: CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
EST: gi|124779313|gb|EH869256.1|EH869256
EST:     CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGNGAAAGCTGTTGTCCAG                         GTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC
genomic: CGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAGgtttatgatc ... tggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacatgctatagagatcaatgccctcaatgattaatccatctatggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTCACAGGAGAG
                               gattaat  putative branch site (score: 3)
                                                ctttc  putative PPT
                            aatgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatgatctttcatattattgtaaatgttaattctgcataacactagtttgttgaatctaggtgatgaatgcacatgctatagagatcaatgccctcaatgattaatccatctatggctttcagGTTTTTGAAGGAACATCTGGGATTGACAACAAGTTTACCACCGTGCAATTCACAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA