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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatatttttaagccaacatttgttttgaacaatgaccacttaccaagaggtgcaacttggtttaaatttgtcatctaatgcttcacacttcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAAGCTTACTGATTTGTTTGACTT

Basic information

species Glycine max
transcript GLYMA06G05900.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05900.3 (Glycine max), 3'ss of exon 13
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 13
caatatttttaagccaacatttgttttgaacaatgaccacttaccaagaggtgcaacttggtttaaatttgtcatctaatgcttcacacttcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAAGCTTACTGATTTGTTTGACTT
        |    ||||| ||   ||       |  |   || |  | ||   | |||  |||    ||  | ||| ||   ||   |    | | | |||||| | ||||| || ||| | |  || ||||| ||||| |||||||| ||||||||||| ||||||||  |
-------gtatgaccaaccttctcttcac---ttctctttttgcatacagtcactactaagttgtgtttccttatc-aactatttgtaaaatattcatagGGAACTCAATGATAATCATCTCACGGGTCATATACCACCAGAGCTTGGGAAGCTTACTGACTTGTTTGATCT
















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|208314541|gb|GE113877.1|GE113877
EST:     ACTGGCCTCATCCCCCCAGTACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
EST: gi|207823198|gb|GD794923.1|GD794923
EST:     ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
EST: gi|208062441|gb|GD860519.1|GD860519
EST:     ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
EST: gi|207746621|gb|GD721608.1|GD721608
EST:     ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
EST: gi|193451692|gb|FK419848.1|FK419848
EST:     ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
EST: gi|193652004|gb|FK597274.1|FK597274
EST:     ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
EST: gi|208278224|gb|GE075721.1|GE075721
EST:     ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTT                         GGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA
genomic: ACTGGCCTCATCCCCCCAGAACTTGGAAATATGACAAACCTTCACTATTTgtaagatgct ... tcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaggtgcaacttggtttaaatttgtcatctaatgcttcacacttcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAAGCTTACTGATTTGTTTGACTT
                            atctaat  putative branch site (score: 3)
                tttaaatttgtcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatatttttaagccaacatttgttttgaacaatgaccacttaccaagaggtgcaacttggtttaaatttgtcatctaatgcttcacacttcaattacagGGAATTGAATGACAACCATTTAAGTGGACATATCCCACCTGAGCTTGGAAAGCTTACTGATTTGTTTGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT