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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtataacatgccatagaacttaagaccctttctcttctctggaagcaaaatctagtttcacttaaatatattgctcattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCATCAAGGCGAGGAAGTTGTCTAGTGCGCTCTCTGCTGCTAGCTCTGCTTGT

Basic information

species Arabidopsis thaliana
transcript AT1G04410.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g33800.1 (Oryza sativa), 3'ss of exon 4
gtatgtataacatgc--catagaacttaagaccctttctcttctctggaagcaaaatctagtttcacttaaatatattgctcattct----gtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCATCAAGGCGAGGAAGTTGTCTAGTGCGCTCTCTGCTGCTAGCTCTGCTTGT
|||  |   | ||||  |||| |    || |   |   | || | |     || | |    || ||  |  || || || |  |         |||||  |    ||||| |||||||| || || || ||||| || || ||||||||||||||||||   || ||||| || |||||||| |||||||| || 
gtaaatcagaaatgctgcatatattaaaaaaaagtagtttttgtttttgttcatatttccattgcatatggatttaatggtggtctctcaaacagGTTAAATACGGAATTCATCTCTACCGTCCAGCAGCGTGGTGCCGCCATCATCAAGGCGAGGAAGCAATCCAGTGCCCTATCTGCTGCCAGCTCTGCATGC

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G415359_T03 (Zea mays), 3'ss of exon 1
------gtatgtataacatgcc---atagaacttaagaccctttctcttctctggaagcaaaatctagtttcacttaaatatattgctcattctgta---gGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCATCAAGGCGAGGAAGTTGTCTAGTGCGCTCTCTGCTGCTAGCTCTGCTTGT
        || |  || || |    |||  |||      |  |  | | ||       || ||  | |  | | |    |  | |  |  || | ||   || |  | || ||||| ||| | || || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||||| ||||||||||||||||||
aatcagaaattttcaaaatacttggatatcactgtttgtcgctattttcctggtaggtcagaagttggaattaat-ggtttcactcttttttttataacagGCTTAATGGTGAATTCATCACAACTGTCCAACAGCGTGGTGCTGCAATCATTAAAGCGAGAAAGTTCTCCAGTGCTCTCTCGGCTGCTAGCTCTGCTTGT

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G415359_T02 (Zea mays), 3'ss of exon 4
gtatgt-ataacatgccatagaacttaag----accctttctc-----ttctctggaag--caaaatctagtttcacttaaatatattgctcattctgt---agGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCATCAAGGCGAGGAAGTTGTCTAGTGCGCTCTCTGCTGCTAGCTCTGCTTGT
|||  | | ||  |  || |  ||||       ||  ||| ||     ||  |||| ||  || ||  | |  | | |    |  | |  |  || | |   ||| |  | || ||||| ||| | || || ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||||| ||||||||||||||||||
gtaaatcagaaattttcaaaatacttggatatcactgtttgtcgctattttcctggtaggtcagaagttggaattaat-ggtttcactcttttttttataacagGCTTAATGGTGAATTCATCACAACTGTCCAACAGCGTGGTGCTGCAATCATTAAAGCGAGAAAGTTCTCCAGTGCTCTCTCGGCTGCTAGCTCTGCTTGT

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|124909019|gb|EH983099.1|EH983099
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGC
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGC
EST: gi|125275181|gb|EL289266.1|EL289266
EST:     TGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: TGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|125044385|gb|EL116654.1|EL116654
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAA
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAA
EST: gi|47830669|gb|CK120353.1|CK120353
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCA
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCA
EST: gi|124849500|gb|EH933937.1|EH933937
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAG
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAG
EST: gi|47828241|gb|CK117925.1|CK117925
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAAC
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAAC
EST: gi|125119243|gb|EL167562.1|EL167562
EST:     CCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: CCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|125197110|gb|EL212064.1|EL212064
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTA
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTA
EST: gi|124842391|gb|EH926828.1|EH926828
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTG
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTG
EST: gi|125302009|gb|EL316094.1|EL316094
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAG
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAG
EST: gi|124918163|gb|EH992028.1|EH992028
EST:     CTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: CTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|124720719|gb|EH812121.1|EH812121
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTAT
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTAT
EST: gi|47828264|gb|CK117948.1|CK117948
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAAAATTTATCTCTACAGTTCAACAA
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAA
EST: gi|164185101|gb|ES010199.1|ES010199
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTAC
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTAC
EST: gi|116378554|gb|EG421146.1|EG421146
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|125044610|gb|EL116879.1|EL116879
EST:     GAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: GAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|116378552|gb|EG421144.1|EG421144
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|47831346|gb|CK121030.1|CK121030
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|125285606|gb|EL299691.1|EL299691
EST:     CGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCA
genomic: CGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCA
EST: gi|86080897|gb|DR376654.1|DR376654
EST:     CGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: CGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
EST: gi|116376802|gb|EG419394.1|EG419394
EST:     ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATG                         GTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT
genomic: ACCTCGTCTGGAGAGAAGCCTGTCCGTGAGCTCGTCAAGGACGATGCATGgtatgtataa ... cattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttctctggaagcaaaatctagtttcacttaaatatattgctcattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCATCAAGGCGAGGAAGTTGTCTAGTGCGCTCTCTGCTGCTAGCTCTGCTTGT
                                           ctcattct  CT-rich tract
                         tttcacttaaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtataacatgccatagaacttaagaccctttctcttctctggaagcaaaatctagtttcacttaaatatattgctcattctgtagGTTGGACGGAGAATTTATCTCTACAGTTCAACAACGTGGAGCTGCAATCATCAAGGCGAGGAAGTTGTCTAGTGCGCTCTCTGCTGCTAGCTCTGCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT