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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcagactacccccccccctctcattgaccttctctggcctataaattatgtctataccatctaatattgtatataatgtatagttttggttgcatcctgttatgctattaaatttcatatttcatatcctttacaatggcagcatattttaattgtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCTGTCTTGAATCTTTTAATATATAATGTAGCTGGAGGCGGTGAAAGCCATC

Basic information

species Glycine max
transcript GLYMA13G34570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g01410.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtcagactacccccccccctctcattgaccttctctggcctataaattatgtctataccatctaatattgtatataatgtatagttttggttgcatcctgttatgctatta-aatttcatatttcatatcctttacaatggcagcatattttaattgtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCTGTCTTGAATCTTTTAATATATAATGTAGCTGGAGGCGGTGAAAGCCATC
|||||| |    || |     |  ||  |||    |    |  | ||  || ||  |    |  | |  |       | ||| || ||   |  |       | | ||  ||||  |||||| || |   |||  || |   ||     || ||||   | |  || |||||| | ||| |  || | ||||   |||||||||||| |||||| |||||||| |||||||| || |||||||||||    || || || || |||||| 
gtaagtta----actctggtacagct--ttggttattaaggaacaatctatgatagcatacctgtttcttggcaatcagaat-taaaggagttatcaagagttttcatcttattttaatttcttaatgtttat--ttaattttga----atgttttggat-ttcttccagGCACTCTCACTTCTTGTTGACTACCACTACTATGGAAGATGGACGTCATCTGTTTTGAATCTCTTGATATATAATGTCTTAGGTGGTGGCGAGAGCCATT
















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|208040698|gb|GD839803.1|GD839803
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCA
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCA
EST: gi|15286732|gb|BI470623.1|BI470623
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
EST: gi|207771499|gb|GD744248.1|GD744248
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
EST: gi|19938576|gb|BQ081785.1|BQ081785
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
EST: gi|298178623|gb|HO024358.1|HO024358
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
EST: gi|208315224|gb|GE117010.1|GE117010
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCT
EST: gi|208281839|gb|GE078565.1|GE078565
EST:     AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTT                         GCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATAGGACTTCATC
genomic: AATTCAAACAGGCATTTATTGCTGCGGCTGTCACATCAATTCTTCTTCTTgtaagtcaga ... gtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAAT-GGACTTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttcatatttcatatcctttacaatggcagcatattttaattgtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCTGTCTTGAATCTTTTAATATATAATGTAGCTGGAGGCGGTGAAAGCCATC
                                     ttttaat  putative branch site (score: 3)
                                  atattttaattgtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcagactacccccccccctctcattgaccttctctggcctataaattatgtctataccatctaatattgtatataatgtatagttttggttgcatcctgttatgctattaaatttcatatttcatatcctttacaatggcagcatattttaattgtgtttacagGCATTGTCAATAGTTATGGACTTTTACTACTATGGAAAATGGACTTCATCTGTCTTGAATCTTTTAATATATAATGTAGCTGGAGGCGGTGAAAGCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG