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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaacattttaagattgaactctttgttttttttcttgcctttgtttctttcgttcttaatgtatctcttctggtctctttctatag

Basic information

species Arabidopsis thaliana
transcript AT4G18710.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G29200.1 (Glycine max), 5'ss of exon 4
ATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaacattttaagattgaactctttgttttttttcttgcctttgtttctttcgttcttaatg--tatctcttctggtctctttctatag---------
|| ||| |||| || ||||| || |||| |||| |||||||||| ||||||||| | |||||||||||| | ||||| ||  ||  ||  |     |||| |     || || ||    | ||  || |      |   ||    |  ||  |||| | || || | |           
ATTTTCAGGGGGCTGGCTTATATCCACACTGTTCCTGGAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgctta-tatgctcttgctgaa-tggaaattattattaggactttctttccgaatagtaggaactatttcctgctctgatgtcattttgtgtattctctag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 5
ATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaacattttaagattgaactctttgttttttttcttgcctttgtttct--ttcgttcttaatgtatctc-ttctggtctctttctatag---------
|| ||| | || || ||||| || |||| |||| |||||||||| ||||||||| | |||||||||||| | ||||| ||  ||  || |      ||||        || || |   | |||| |||||   | ||    | | | ||    |||| | || || | |           
ATTTTCAGTGGGCTGGCTTATATCCACACTGTTCCTGGAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgctta-tatgtgcttgctgaatgga--aattattattaggactttctttctgaatagtaggaactatttcctgctctgatgtcattttgtgtattctctag

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 5
ATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaacattttaagattgaactctttgttttttttcttgcctttgtttctttcgttcttaatgtatctcttctggtctctttctatag
|| ||| |||| || || || || |||| |||| |||||||||| || || ||| | ||||||||||||||||| ||||||      || |  || ||      ||| ||    |  ||     ||  |    |   | |||| ||   || | | || | |||| ||
ATTTTCAGGGGCCTGGCATATATCCACAGTGTTCCTGGAGTTTGCCATAGGGATTTGAAGCCTCAAAATCTTCTAgtatgttc----ttctctgactg------ttgcttaaaataatga----gtcacaactgca-tcaatgaattaatttttggct-tctctacag

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|86056751|gb|DR352508.1|DR352508
EST:     AATGNNNNCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTTCTG                         GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAA
genomic: AATGTTG-CTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTT-CTGgtatgtgtaa ... ctttctatagGTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAA
EST: gi|125042974|gb|EL115243.1|EL115243
EST:     ACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTG                         GTTGATCCTCTTACTC
genomic: ACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaa ... ctttctatagGTTGATCCTCTTACTC
EST: gi|125092868|gb|EL150668.1|EL150668
EST:     TAAAGCCTCAAAATCTTCTG                         GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAA
genomic: TAAAGCCTCAAAATCTTCTGgtatgtgtaa ... ctttctatagGTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAA
EST: gi|125047580|gb|EL119849.1|EL119849
EST:     AGATCTAAAGCCTCAAAATCTTCTG                         GTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAA
genomic: AGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaa ... ctttctatagGTTGATCCTCTTACTCATCAAGTCAAAATCTGTGACTTTGGCAGTGCGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTCCGGGGACTTGCTTACATTCACAATGTTGCTGGAGTTTGTCACAGAGATCTAAAGCCTCAAAATCTTCTGgtatgtgtaacattttaagattgaactctttgttttttttcttgcctttgtttctttcgttcttaatgtatctcttctggtctctttctatag

- - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - -  GAGATC