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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcctcattgcccagaccatgcctgttactgacactcacaagcaattacaaacacgataaacaagtttcgtaatctgtgctggctttttggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACAT

Basic information

species Arabidopsis thaliana
transcript AT4G23470.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G060564_T02 (Zea mays), 3'ss of exon 5
gtaagtatcctcattgcccagaccatgcctgt-tactgacactcacaagcaattacaaacacgataaacaagtttc----gtaatctgtgctggcttt--ttggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACAT
||||     ||     |  | |   | ||||| |  ||  | |||    |   |  |       |   |    |||    || |  ||  |||  | |       | || |||| |||||| | |||||    ||||| |||||||| ||||| |||||||||  |||||| ||||  || ||||||||||| ||||| ||||| || |  |
gtaacaccacttgcctcttaaat--ttcctgtctgatgcgattcaacgtcctgtggagggttcctgttctttcttccgatgtcacttggactgaatataaccttttatgcagGGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATT
















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|124958722|gb|EL033446.1|EL033446
EST:     GCAAGTATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGG
genomic: GCAAG-ATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGG
EST: gi|125189739|gb|EL204693.1|EL204693
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCA
EST: gi|116434599|gb|EG477191.1|EG477191
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|86038879|gb|DR334634.1|DR334634
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|301501098|gb|HO206638.1|HO206638
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|124789102|gb|EH878781.1|EH878781
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTC
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTC
EST: gi|164048543|gb|ES145217.1|ES145217
EST:     TTCAAACGACAAAATGTGACAACTGCATCATT                         GGTCTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|86038878|gb|DR334633.1|DR334633
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATNNNNCAACTGCATCATT                         GGTTTCATGGCTTGCCTCAGCCAAGTNGG-TTGCATATTCTCCATAGTTGC
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGT-GGCTTGCATATTCTCCATAGTTGC
EST: gi|86038882|gb|DR334637.1|DR334637
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|301502433|gb|HO207973.1|HO207973
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|86038877|gb|DR334632.1|DR334632
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         T
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtag-
EST: gi|86038877|gb|DR334632.1|DR334632
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         T
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtag-
EST: gi|124728187|gb|EH819589.1|EH819589
EST:     CCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: CCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
EST: gi|116434598|gb|EG477190.1|EG477190
EST:     TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT                         GGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA
genomic: TGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATTgtaagtatcc ... ggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacaaacacgataaacaagtttcgtaatctgtgctggctttttggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACAT
                                       ctttttg  CT-rich tract
            ataaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcctcattgcccagaccatgcctgttactgacactcacaagcaattacaaacacgataaacaagtttcgtaatctgtgctggctttttggctgtgtagGGTTTCATGGTTTGCCTCAGCCAAGTGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC