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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttgtgcccttcagtccctgtgcagggtgcctttattgcgtgacaattacttacgctgcctatgttaacaatccttaatcttgtgatggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCACCAAA

Basic information

species Glycine max
transcript GLYMA13G30670.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G30670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g00640.t01 (Vitis vinifera), 3'ss of exon 7
gtaaagttgtgcccttcagtccctgtgcagggtgcctttattgcgtgacaattacttacgctgcctatgttaacaatccttaatcttgtgatggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCACCAAA---
|||| |||        ||  |||||    || |  |||||   | |     || |||  |    |     |  |   | |  |  ||   |||  |   ||||  |||||||||||||||| ||||| || ||||||||||| |||     ||||     
gtaaggttac------cacaccctg----ggttttctttaccactt-----ttccttttgggaacaccact--ctgacttccactttacaatgttggaaagGTCAATTTGGTTAATGATGGTCCAGTCACAATGCAGCTTGACTCATCGCAACCATCCAA
















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|298199178|gb|HO042541.1|HO042541
EST:     ACGGTGTATTCGGAGCAATGATGAAG                         GTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCA
genomic: ACGGTGTATTCGGAGCAATGATGAAGgtaaagttgt ... tggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCA
EST: gi|207754888|gb|GD727341.1|GD727341
EST:     ACGGTGTATTCGGAGCAATGATGAAG                         GTAGATTTGGTTAATGATGGACCAGTTACCA
genomic: ACGGTGTATTCGGAGCAATGATGAAGgtaaagttgt ... tggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCA
EST: gi|13478787|gb|BG508130.1|BG508130
EST:     ACGGTGTATTCGGAGCAATGATGAAG                         GTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCA
genomic: ACGGTGTATTCGGAGCAATGATGAAGgtaaagttgt ... tggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCA
EST: gi|298182728|gb|HO031463.1|HO031463
EST:     ACGGTGTATTCGGAGCAATGATGAAG                         GTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCA
genomic: ACGGTGTATTCGGAGCAATGATGAAGgtaaagttgt ... tggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCA
EST: gi|208305147|gb|GE102820.1|GE102820
EST:     ACGGTGTATTCGGAGCAATGATGAAG                         GTAGATTTGGTTAATGATGGACCAGTTACCA
genomic: ACGGTGTATTCGGAGCAATGATGAAGgtaaagttgt ... tggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaattacttacgctgcctatgttaacaatccttaatcttgtgatggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCACCAAA
                   tatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagttgtgcccttcagtccctgtgcagggtgcctttattgcgtgacaattacttacgctgcctatgttaacaatccttaatcttgtgatggagagcagGTAGATTTGGTTAATGATGGACCAGTTACCATGCAGCTTGATTCAAATTCACCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT