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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaaaaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttgatatcaaatgttgcttgataacatttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT

Basic information

species Glycine max
transcript GLYMA05G03770.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03770.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g01030.3 (Oryza sativa), 3'ss of exon 8
gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaaaaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttgatatcaaatgt-tgcttgataacatttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT
                                             || | |||  | ||    |  | ||   |  |   ||| |        |||    |     | |   || |||| || ||       ||   ||||||||||| |||||||| |||||| |||| || ||||||||||| |||||||||||||                                          
-------------------------------------------gtaagtgatt-tagaattagctaccctcattggttttcattc--------cttgagatgacagtcactacacatgtatgtttttccctcttcaacagGACCCTGATCTGATGGCAGCATTTGGTGACCCTGAGGTTATGGCAGCTCTTCAAGATG------------------------------------------

upper sequence: GLYMA05G03770.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G134806_T01 (Zea mays), 3'ss of exon 9
gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaaaaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttgatatcaaatgttgcttgataacatttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT
|||||| |   |   |  | | ||| ||  | || || ||        || ||        ||  ||   | || ||  ||||| |            |||  | ||  ||  |    ||||||  |    |||  ||||||||||| |||||||| ||||| ||||| || ||||| ||||| ||| | ||||||||||                                       
gtaagtga--ttaaccagttgctgtcttcct-tggttatgt-------tcgttt-------tttatccacttctgatacacatgaa------------tctcctttttgtacaatgatttgctttctt-tgtttaccagGACCCTGACCTGATGGCAGCATTCAGTGACCCAGAGGTCATGGCGGCTTTACAAGATGGTATG-------------------------------------

upper sequence: GLYMA05G03770.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G22670.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaaaaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttgatatcaaatgtt--gcttgataacatttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT
                                                        || |    || | |    | |    ||   || | |  ||    ||   |||| ||     | |  | ||||||    |   ||||| ||||| || ||| |||||||||| || || || || |||||||||||||||||||                                          
------------------------------------------------------gtaagagcgactatttgtgaattaccaatatccagagtttttgaagttaaattgacattgtgagattggtttgatatttgtgagcagGATCCTGAGCTAATGACGGCATTTAGCGACCCTGAAGTCATGGCTGCTCTTCAAGATG------------------------------------------

upper sequence: GLYMA05G03770.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S9_386V6.3 (Physcomitrella patens), 3'ss of exon 9
-------------------------gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaa--aaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttga------tatcaaatgttg----cttgataacatt----tctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTC--TTTTTGTATT
                          |   |    |    || | ||| | | |   | ||    |||    |    ||  |   | ||       || ||  || |   | |  |  ||||| ||  ||||| ||      |   |  | ||     || |  ||  ||    || |||||||| ||||| ||||| ||||||  |||||| || |||||||| |||||||||||||||| | || |  |||   | || |  |  | |  | ||| || |
gtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctt-tttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATGGTA-TGATTA-CTCTTTCGCTTAGAACTGTGCGATGTTTTTAAT

upper sequence: GLYMA05G03770.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S9_386V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaa--aaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttga------tatcaaatgttg----cttgataacatt----tctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT
                          |   |    |    || | ||| | | |   | ||    |||    |    ||  |   | ||       || ||  || |   | |  |  ||||| ||  ||||| ||      |   |  | ||     || |  ||  ||    || |||||||| ||||| ||||| ||||||  |||||| || |||||||| |||||||||||||                                          
gtaagcattagcatagagcattaaaatgcattcgcccattctcttgatctatgtcgatcctacctagagctcaatggtattatcgatataataacttttctgttggatgcgaatgctgtgctt-tttgtgtctagaccgagttgcgacgttttaatgtctcgtcaaacttgtgatcgcagGACCCAGAACTTATGGCTGCATTTTCTGATCCAGAAGTTATGGCAGCTCTTCAAGATG------------------------------------------

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|193540896|gb|FK496058.1|FK496058
EST:     GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGT                         GACCCTGAACTGATGGCGGACATTTAGTGATCCGGAGGTTATGGCTGCTCT
genomic: GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGTgtaagtaaat ... catttctcagGACCCTGAACTGATGGCGG-CATTTAGTGATCCGGAGGTTATGGCTGCTCT
EST: gi|193574189|gb|FK533049.1|FK533049
EST:     GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGT                         GACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
genomic: GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGTgtaagtaaat ... catttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
EST: gi|208259864|gb|GE059306.1|GE059306
EST:     GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGT                         GACCCTGAGCTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
genomic: GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGTgtaagtaaat ... catttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
EST: gi|208032364|gb|GD828147.1|GD828147
EST:     GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGT                         GACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
genomic: GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGTgtaagtaaat ... catttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
EST: gi|193467408|gb|FK432521.1|FK432521
EST:     GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGT                         GACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
genomic: GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGTgtaagtaaat ... catttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTT
EST: gi|208301818|gb|GE099384.1|GE099384
EST:     GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGT                         GACCCTGAACTGATGGCGGCATTTAGTGAT
genomic: GCATGCCTGGAGGGGTGCCTGGAAACATTGATTTTAGCAAAATCTTGAGTgtaagtaaat ... catttctcagGACCCTGAACTGATGGCGGCATTTAGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacaatgcttattcttgtcttgatatcaaatgttgcttgataacatttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT
                                       tgataac  putative branch site (score: 2)
                                             catttctc  CT-rich tract
                        atatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaatctggactttggatgtttttgtgtgcttttgagaaaaaatcattacaaaaaattcctctcttcctaatgaacatgcacacaatgcttattcttgtcttgatatcaaatgttgcttgataacatttctcagGACCCTGAACTGATGGCGGCATTTAGTGATCCGGAGGTTATGGCTGCTCTTCAAGATGGTAATTATCAGTTCTAATGTTTGGTTCCATTCTTTTTGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG