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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaactattcccaaaataaattgtttctggattctccttttccgtaaattttcctctcttattattactctttcccgtggcacttattttaggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

Basic information

species Glycine max
transcript GLYMA11G08350.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08350.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
tcaaactattcccaaaataaattgtttctggattctccttttccgtaaattttcctct--cttattattactctttcccgtggcacttatttt---aggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG
                 ||| | ||   ||       |||   | |   || || ||   | ||     |||| |  ||    |||||| |||   |||| |||||||||||  | || |||||  ||||||| |||||||| ||||||||||||||||||
----------------gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacc-catcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG

upper sequence: GLYMA11G08350.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
-----tcaaactattcccaaa-ataaattgtttctggattctccttttccgtaaattttcctctcttattattactct--ttcccgtggcacttattttaggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG
     |  |     |   |    | |     | |    || |  ||  |    ||    | |     | |   | |||  ||  |    |  ||  || ||||||||||||||||||| || |||||||||||||| |||||||| |||||||||||||||| |
ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatc-ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
















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|57573973|gb|CX546948.1|CX546948
EST:     AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAA                         T
genomic: AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgattgtct ... taggcaatag-
EST: gi|57573973|gb|CX546948.1|CX546948
EST:     AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAA                         T
genomic: AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgattgtct ... taggcaatag-
EST: gi|57574227|gb|CX547202.1|CX547202
EST:     GGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAATAG-                         AAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCT
genomic: GGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATG---T-GAgtgattgtct ... taggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCT
EST: gi|209711275|gb|BW665327.1|BW665327
EST:     GACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAATAG-                         AAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCT
genomic: GACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATG---T-GAgtgattgtct ... taggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCT
EST: gi|14196069|gb|BE657919.2|BE657919
EST:     TTGAACTTGGGTCATACATTTGGTCATGCAATAG-                         AAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCT
genomic: TTGAACTTGGGTCATACATTTGGTCATG---T-GAgtgattgtct ... taggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCT
EST: gi|151408017|gb|EV277832.1|EV277832
EST:     AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAA                         T
genomic: AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgattgtct ... taggcaatag-
EST: gi|151408017|gb|EV277832.1|EV277832
EST:     AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAA                         T
genomic: AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgattgtct ... taggcaatag-
EST: gi|151401299|gb|EV271113.1|EV271113
EST:     AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAA                         T
genomic: AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgattgtct ... taggcaatag-
EST: gi|151401299|gb|EV271113.1|EV271113
EST:     AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGCAA                         T
genomic: AAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgattgtct ... taggcaatag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattttcctctcttattattactctttcccgtggcacttattttaggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG
                                      cttatttt  CT-rich tract
              ttattattactcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaactattcccaaaataaattgtttctggattctccttttccgtaaattttcctctcttattattactctttcccgtggcacttattttaggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
tcaaact
- - - - - cccaaaa
- - - - - - - - - - - -gtttctg