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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattcactcttctacttcttctttgccttatcaagctctcttattagactatttcacaagtttgttcactgctttaacagGGTTCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTTTGATTCCGGAGTCACCATTTTACCTGGAAGGAGAAGGCGGACTGTTTGA

Basic information

species Arabidopsis thaliana
transcript AT4G26270.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 10
--------------------------------------gtgagaattcactcttctacttcttctttgccttatcaagctctcttattagactatttcacaagtttgttcactgctttaacagGGT-TCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTTTGATTCCGGAGTCACCATTTTACCTGGAAGGAGAAGGCGGACTGTTTGA-----------------------------------------
                                       |  || |  | | ||||   | ||| |   ||        |     ||| ||| |  |  ||   || ||| |  |   ||  |    || ||   || |  |   ||||  |    | ||     |||||||| || ||||| ||||||||||||||  ||||||| || || |||||||||||                                         
gtaagttaatgctttatatctatgtcgttctttagtttcttcgagtcaaatattctgtgtattcatgttctgggtgcagtaatgcattggaccacctagcattcttcttctccacg--aatggtacctcctattcat-tgggtttctctgtcttctatag-

upper sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 10
------gtgagaa-ttcactcttctacttcttctttgccttatcaagctctcttattagactatttcacaagtttgttcactgctttaacagGGTTCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTTTGATTCCGGAGTCACCATTTTACCTGGAAGGAGAAGGCGGACTGTTTGA-----------------------------------------
       ||| |  || ||   |  |  |  | ||   ||||      | | || |||  ||   || |  |   |   | |  |||  ||    |||  |  |    | | | | |  | |     ||   |||||||||||||||||| ||||| |||||||| ||||| ||||| || ||| || || |                                         
gtaagtatgacacctttacctgtagatgttatgttctgcttagtctattatttttttattcttgctcgcttgccggagtatttttttttcaaacatcagtgttagaattacgatttt--ccattttcgaca-gGACTGCTGTTTGATTCCAGAGTCTCCATTTTATCTGGATGGAGAGGGTGGATTGCTTCAATATGTAGAGAAGAGGCTGAAAGAGAACAAGCACATGGTTA
















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|301503229|gb|HO208769.1|HO208769
EST:     GAGTATAGAGAATGGTATCGGAGTTGTCAAGCTTATGGGTCGCTACAGCG                         GGTTCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTT
genomic: GAGTATAGAGAATGGTATCGGAGTTGTCAAGCTTATGGGTCGCTACAGCGgtgagaattc ... gctttaacagGGTTCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttatcaagctctcttattagactatttcacaagtttgttcactgctttaacagGGTTCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTTTGATTCCGGAGTCACCATTTTACCTGGAAGGAGAAGGCGGACTGTTTGA
                                           ctgcttt  CT-rich tract
               ttattagactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaattcactcttctacttcttctttgccttatcaagctctcttattagactatttcacaagtttgttcactgctttaacagGGTTCATAGCGATGTATGCCACTCTAGCAAGCAGAGATGTGGACTGCTGTTTGATTCCGGAGTCACCATTTTACCTGGAAGGAGAAGGCGGACTGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA