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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgccttgcctttgataattttctttatttcctgaaatggaatttttgcttctcttttttattttttatttttacattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG

Basic information

species Glycine max
transcript GLYMA11G12260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g50616.1 (Oryza sativa), 3'ss of exon 2
----------------------gtgtgccttgcctttgataattttctttatttc--ctgaaatggaatttttgcttctctttttta----ttttttat-----ttttacatttta------tagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
                      | ||  |      |||  | || || ||| | |  | ||||    |   |||||| | |  ||||    || || ||     | | |||| |||      |||||||||||||||| | || ||||||||||| | |||||| ||||||||| | || |||||   ||||||||||||||| ||  ||||||  ||   |   
gtgcaatttttttctgatctcagagtcacagttacttgg-atttctccttactcctgcagaaaattcagcgttgcttatttgatttaaaatttcttcatgtgcctatgacatgttacacatgtagGTTCCTGAAAGCGCGAAAATTTGATATTGATAAAGCAAAACATATGTGGTCGGAAATGCTTAGATGGAGGAAGGAGTTCGGGGCTGACAACATAGAG---

upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 3
gtgtgccttgcctttgataattttctttatttcctgaaatggaatttttgcttctcttttttattttttatttttacattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
  ||   |   |  |  || ||  | | ||||  | ||    | |     | |     |    |   | |||  |   || | ||| || || ||||| ||||  ||||| ||||| | ||||||||| |||||| |||| |||||  |||||||||||||||  ||||| || || ||| | |||
--gtatatataccctattacttaccatcatttttttaacccaactgcaaacatgctgatgacttgactaattgat---ttgtgtagATTTCTAAAAGCAAGGAGATTTGACATTGAGAAAGCAAAGCAAATGTGGACTGACATGCTTAAATGGAGGAAGGAGTACGGTACAGATACAATTGTTGAG

upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G157043_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------gtgtgccttgcctttgataattttctttatt-------tcctgaaatggaatttttgcttctctttt---ttattttttatttttacatttt------atagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
                                                        || |   || |||     |  ||| |  ||          |   ||| ||||||   |  ||  |||   |||  |||| ||| ||    ||       ||||||||||||||| || || ||| ||||||| | |||||| ||||||||| | || |||||   |||||||||||| |||||| |||||| |||   |   
gtattgctgcatctgatttgctcatcttaagtttcttggttcttctcttctgtcaagtttttatttcctgcacaatatttttacatggaaaaaactcatgaatagaatttcgcccccttatttggtttaacttttctttctatgccttttacatgtagGTTCCTGAAAGCAAGAAAATTTAATATTGACAAAGCAAAACATATGTGGTCAGAGATGCTTAGATGGAGGAAGGAATTTGGTGCTGACAATATAGAG---

upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 3
------gtgtgccttgcctttgataattttctttatttcctgaaatggaatttt----tgcttctcttttttattttttat--ttttacatt--ttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
       ||| ||     |||  || | |    |||| | | || |    |||     ||  |   | |   ||| || |     ||| |||  ||  |||||| ||||||| ||||||||||||||||| | ||||||||| |||||| |||||||| | || ||||||||||| |||||| ||||||| ||| |||||
tattttatgttccaactattttttattatatggtattgcttcaactatgttttcataatgagtaggtataacattgttaagagcattatattacttgcagGTTCTTGAAAGCAAGGAAGTTTGATATTGAGAAAGCAAAGCACATGTGGACTGATATGATTCAGTGGAGGAAGGATTTTGGTGCTGACACAATTTTGGAG

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|193601711|gb|FK552192.1|FK552192
EST:     AATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: AATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|208265768|gb|GE062241.1|GE062241
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|208288228|gb|GE083107.1|GE083107
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|213588301|gb|DB967787.1|DB967787
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|193633223|gb|FK578819.1|FK578819
EST:     TGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: TGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|209713242|gb|BW681781.1|BW681781
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAGGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|8283332|gb|BE020893.1|BE020893
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGGTAAG                         GTGGCTGGAAGCGGAG-AAGTATGATATT
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCG-AGGAAGTTTGATATT
EST: gi|213590510|gb|DB968088.1|DB968088
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAGGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|213603344|gb|DB966603.1|DB966603
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGANAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|193369813|gb|FK337173.1|FK337173
EST:     TTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
genomic: TTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGC
EST: gi|209719529|gb|BW651007.1|BW651007
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAGCGAGGAAGTTTGATATTGAA
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAA
EST: gi|298171644|gb|HO021236.1|HO021236
EST:     ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAG                         GTTCCTGAAAG
genomic: ATGGAAGAATTGCTTCCTGAGAAACACGATGATTACCACGTCATGTTAAGgtgtgccttg ... cattttatagGTTCCTGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgaaatggaatttttgcttctcttttttattttttatttttacattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG
             tttttgcttctctttt  CT-rich tract
           aatttttgcttctctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgccttgcctttgataattttctttatttcctgaaatggaatttttgcttctcttttttattttttatttttacattttatagGTTCCTGAAAGCGAGGAAGTTTGATATTGAAAGAGCAAAGCATATGTGGGCTGATATGCTACAATGGAGGAAGGAGTTTGGTACTGACACTATTATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG