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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

taaattgacctacttttcagttccatttatatttgttatcagtccttgttcatctgaattttgagcatttaaaaattgtgccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTTCTTAAAAACAAGGGTCTATGTGGACAATTAACAGTGAGCAGAGAGGATC

Basic information

species Glycine max
transcript GLYMA18G35390.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G35390.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 5
---taaattgacctacttttcagttccatttatatttgttatcagtccttgttcat-ctgaattttgagcatttaaaaattgtgccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTTCTTAAAAACAAGGGTCTATGTGGACAATTAACAGTGAGCAG-AGAGGATC---
     ||||  |  || ||||  ||   ||  ||   | ||| | | |||  ||   ||| | ||   |  ||      || ||   |||||||||||||||||||||||||| || || ||||| |      |||  |    | | ||      ||  |  |  |||         |||  |   | |  |||   
gtaacaattccctcacctttcc-ttttgttcctaac-gctatgaattcttcctcggactgtaatt---gttttcccccgttatgat-tgcagCTGGAAGAACAACAAAAAGCTCCAATTACCAGCTTA-----ATTTCTAAAGTTTCAATGCTCGGGAACCCTACGGATTCGATTTGGTGCCCGACAAAACATCTAC
















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|193526330|gb|FK480720.1|FK480720
EST:     TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGC                         TGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
genomic: TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGGtaaattgacc ... gccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
EST: gi|21256179|gb|BQ453067.1|BQ453067
EST:     TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGC                         TGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
genomic: TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGGtaaattgacc ... gccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
EST: gi|7233537|gb|AW568942.1|AW568942
EST:     TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGC                         TGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
genomic: TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGGtaaattgacc ... gccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
EST: gi|192316960|gb|FK010891.1|FK010891
EST:     TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGC                         TGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
genomic: TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGGtaaattgacc ... gccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
EST: gi|11413728|gb|BF425739.1|BF425739
EST:     TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGC                         TGGAAGAACAACAAAAAGCTTCATTTGCCA
genomic: TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGGtaaattgacc ... gccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCA
EST: gi|22929555|gb|BU546694.1|BU546694
EST:     TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGC                         TGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT
genomic: TTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGGtaaattgacc ... gccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatcagtccttgttcatctgaattttgagcatttaaaaattgtgccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTTCTTAAAAACAAGGGTCTATGTGGACAATTAACAGTGAGCAGAGAGGATC
                      aattttgagcatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattgacctacttttcagttccatttatatttgttatcagtccttgttcatctgaattttgagcatttaaaaattgtgccgtgcagcTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTGTATTCTTCTGTTCTTAAAAACAAGGGTCTATGTGGACAATTAACAGTGAGCAGAGAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT