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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggttgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG

Basic information

species Glycine max
transcript GLYMA12G36520.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 18
ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggttgggt-caaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
     ||||| ||||   |    |||   | |    |||  | ||   || | ||   |  ||  ||    |     |||||  | |||    |  ||||||||||||| || || ||| ||||||| ||||||||||| || |||||||| ||||| || ||||||||||| |||
ggctcttcattgttaacagggttgttctcttgtaaaagctatgtcttgaactgaaagtgtctaaagggaaagagttgatgttg-tggttcctatactgcagGTTGATGCTGCCCTAGATCTGAGCCATACACAAAACATTGGTAGAATGATCAAGGCGCATTTTCCGCACTCCCAG

upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggttgggt-caaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
 || | || ||  | | |||||  | |||||  |  | | ||       | |  ||    | ||||      | ||| ||     ||||       ||||||||||||| ||||||||| |||||||||| |||||||| || |||||||| |||||||| |||||||||||||||
ttacagtcttgtatgtctgatac-tctgatgcctcaaacgtttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG

upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
----------------------------------------------------------------ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggt-tgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
                                                                 ||||||| || | |     |    ||||    || | || || |   |  ||  |  |  |  ||   |  |  || |  | | |  ||| || |  ||||||||||||||||||||| | ||||||||||| |||||||| |||||||||||  |||| || || || || |||
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgac--agtgatcttgaaatgttca-caatcacatgatcttgttgagtttgatgacataagagaagtcatgact--ttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG

upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
--------------------------------------------------------------ataaattcat--ggttatttgataggtttgatggattgagcattctcgataaatta--ataggcatagtggttgggtcaaatgttaattgttt-aattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
                                                                | ||  ||  ||||  || ||   |  ||||  | || || |     |  ||||  ||  ||  ||||    |   ||||  | ||  |||  | |  | ||||||||||||||||||||| | || |||||||| |||||||| ||||||||||  ||||| || || ||||| |||
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatg--tggaacactgattttgcattacaatcagcg-agtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG

upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
-ataaattcatggttatttgataggttt-gatggattgagcattctcgata-aattaataggcatagtggttgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
 |||| | |||    |  |    | |   |||  ||| |  |    || || || |  | || | | ||||      || |||   |  || |  |||||||||| || || |||||||||||||| |||||||| |||||||| |||||||| || |  |||||||| ||||| |||
cataa-tccatttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgt--gtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG

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|58022904|gb|CX709645.1|CX709645
EST:     TTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAG                         GTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATA
genomic: TTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAGgtatgtttta ... attcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATA
EST: gi|193318796|gb|FK284302.1|FK284302
EST:     TTCTGGCACTGCTGCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAG                         GTTGATGCAGCTCTT
genomic: TTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAGgtatgtttta ... attcttgcagGTTGATGCAGCTCTT
EST: gi|58016495|gb|CX703237.1|CX703237
EST:     TTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAG                         GTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATA
genomic: TTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAGgtatgtttta ... attcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATA
EST: gi|193414074|gb|FK376108.1|FK376108
EST:     TTCTGGCACTGCTGCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAG                         GTTGATGCAGCTCTT
genomic: TTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAGgtatgtttta ... attcttgcagGTTGATGCAGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataaattaataggcatagtggttgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
                                              ttcttgc  CT-rich tract
                             aaatgttaattgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggttgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - -ttcatgg
- - - - - - - - - - - - -ttgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttggg