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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcatctgcctcaagagtctttcaatcagcctatgactttcatttccctgtcttatgttgaagtctgacaacgttccataacactagGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG

Basic information

species Arabidopsis thaliana
transcript AT4G23100.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 11
gttaatcatctgcctcaagagtctttcaatcagcctatgactttcatttccctgtcttatgttgaagtctgacaacgttccataacact---agGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG
|||   | |     |       ||    ||||    |||       | |     |  | |  | |    |       ||  ||    ||   ||||  || ||||| ||||  | |||||||||||||||||||| || || ||||||||  |||||||  ||||||| || |||
gtttgcccttaaatttgtatagctgatcatcatggcatgttgacactgtaagcttaatgtaataactatttgttcttttgtatttggcttgcagGTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 10
-gttaatcatctgcctcaagagtctttcaatcagcctatgactttcatttccctgtcttatgttgaagtctgacaac-gttccataacactagGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG
  ||| || | || |||     | |     |  || ||||  |  |||| |   || ||    | |  | || |  | ||    |      ||||| |||| ||||||||| | |||||||||||||||||||| || || ||||||||  ||||||| ||||| || || |||
gtttactcttttgtctc-----tttacatgttggcatatg--tgccattgctaggtattgcaataacttttgtcctctgtattctgcttgcagGTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G01750.2 (Glycine max), 3'ss of exon 10
gttaat--catctgcctcaagagtctttcaatcagcctatgactttca-----tttccctgtcttatgttgaagtctgaca-acgttccataacact----agGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG
|||| |  |   ||  |  | | | |  |    | |   ||  || ||     ||| |    |||   |||  || | ||    ||| ||| |  ||    ||||  || |||||||||| |||||||||||||||||||||||||| || ||||| ||| | |||||  | ||||| || |||
gttagtttctattggtttcacaatttaactggtatctgttgctttgcaatagatttgcagcactttccttgttgtgtaacttgtgttacattattcttttcagGTCAGGCTGAAGAGATATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGGTTATGTGCTTTACCAGCATTTTGG

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
gttaatc---atctgcctcaagagtctttcaatcagcctatgactttcatt----tccctgt-cttatgttgaagtctgacaacgttccataacact----agGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG
|||| |    ||  |  |||  | | |  |    | |   ||  || ||||    |  | |  |||   |||  || | |       |||| |  ||    ||||  || ||||||| || |||||||||||||||||||||||||| || ||||| ||  |||||||  | ||||| || |||
gttagtttctattggtttcacaattttaactggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG

upper sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
gt-taatcatctgcctcaagagtctttcaatcagcctatgactttcatttccctgtcttatgttgaagtctgacaacgttccataacact-agGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG
|| ||  || |||     | | |  |  |||     |||  |||  || |      || |    ||| | ||  |   || |    || | ||||  || |||||||||||||||| ||||| |||||||||||||| |||||||||||| | |||||  ||||||| || |||
gtataggcacctgagatcaaattgatgaaattt-tatatttcttagatgttgtcacctaa----gaaatatgttattttttc----cattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG

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|124873392|gb|EH955037.1|EH955037
EST:     TGCCTTCATATAATGATTGGGAAAACCATCTGACAACAATATTCCCAGAG                         GTTCGGTTGAAGAGATACTTGG
genomic: TGCCTTCATATAATGATTGGGAAAACCATCTGACAACAATATTCCCAGAGgttaatcatc ... ataacactagGTTCGGTTGAAGAGATACTTGG
EST: gi|125226038|gb|EL240123.1|EL240123
EST:     TGCCTTCATATAATGATTGGGAAAACCATCTGACAACAATATTCCCAGAG                         GTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGAT
genomic: TGCCTTCATATAATGATTGGGAAAACCATCTGACAACAATATTCCCAGAGgttaatcatc ... ataacactagGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgactttcatttccctgtcttatgttgaagtctgacaacgttccataacactagGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG
                                           ccataac  putative branch site (score: 3)
     tttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcatctgcctcaagagtctttcaatcagcctatgactttcatttccctgtcttatgttgaagtctgacaacgttccataacactagGTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG