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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcattcctaaatctttctaatcgtgtctccacgatctccaattcgaattccaaattcatcatatctcccgctaagtttcaaatctagtctctactgattaattgtgattttgatttctatgtagCTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTAAAGATGGAAGTGAAGATAATCTGGATCTTTCCAAAGGCTTATATGATGC

Basic information

species Arabidopsis thaliana
transcript AT1G75680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g14040.t01 (Vitis vinifera), 3'ss of exon 1
gtaatcattcctaaatctttctaatcgtgtctccacgat-ctccaattcgaattccaaattcatcatatct--cccgctaagtttcaaatctagtctctactgattaattgtgattttg--atttctatgtagCTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTAAAGATGGAAGTGAAGATAATCTGGATCTTTCCAAAGGCTTATATGATGC
                             | | |   ||  ||||||||  || |    || | |||  ||   | | | | ||||   | || | | || | || | | | |||  |    | ||  || ||||||||| ||||| |||||||||||| | ||||||||| |||| |  ||| |||| |||||||||| |||  | |||||||| |||||  | ||||||||
----------------------------atttacgatatgttccaattcctatactgt-ttgaccatcgctgttctgtttattttc---tttattttttaattatca-tggagatgctactgtgtcattgcagCTGGTAAGTTGGAAAACAATAAGATATCATGGAGAGGAAATTCTGCACTTCAAGACGGAAGTGAAGCTAAATTAGATCTTTCTAAAGGGATGTATGATGC
















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|125265724|gb|EL279809.1|EL279809
EST:     ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAAT                         CTGGTAAATTGGAGAACAATAAG
genomic: ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAATgtaatcattc ... ttctatgtagCTGGTAAATTGGAGAACAATAAG
EST: gi|86052857|gb|DR348614.1|DR348614
EST:     ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAAT                         CTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTA
genomic: ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAATgtaatcattc ... ttctatgtagCTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTA
EST: gi|125172851|gb|EL194800.1|EL194800
EST:     CTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAAT                         CTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTA
genomic: CTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAATgtaatcattc ... ttctatgtagCTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTA
EST: gi|125162652|gb|EL189422.1|EL189422
EST:     ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAAT                         CTGGTAAATTGGAGAACAATAAGAT
genomic: ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAATgtaatcattc ... ttctatgtagCTGGTAAATTGGAGAACAATAAGAT
EST: gi|86052856|gb|DR348613.1|DR348613
EST:     ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAAT                         CTGGTAAATTGGAGAAC
genomic: ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAATgtaatcattc ... ttctatgtagCTGGTAAATTGGAGAAC
EST: gi|125311024|gb|EL325109.1|EL325109
EST:     ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAAT                         CTGGTAAATTGGAGAACAATAAGATA
genomic: ATACGCCGACGCTCTTAAGCTCGCTTTGCAGTTCTTCGATATCCAGAAATgtaatcattc ... ttctatgtagCTGGTAAATTGGAGAACAATAAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaagtttcaaatctagtctctactgattaattgtgattttgatttctatgtagCTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTAAAGATGGAAGTGAAGATAATCTGGATCTTTCCAAAGGCTTATATGATGC
                                            tttctat  CT-rich tract
                           attaattgtgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcattcctaaatctttctaatcgtgtctccacgatctccaattcgaattccaaattcatcatatctcccgctaagtttcaaatctagtctctactgattaattgtgattttgatttctatgtagCTGGTAAATTGGAGAACAATAAGATACCTTGGAGAGGAGATTCAGGTCTTAAAGATGGAAGTGAAGATAATCTGGATCTTTCCAAAGGCTTATATGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA