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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctctaaaacttcgtagtttgttgaacagagaggtagtatagtgtgttttggggtttggcttatctaaccttttgcgaggaatgccaaattatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCAAGTTGCGTCTGCATTGAGAATTGAAGTCAACCGGGGATTTGCTGTTTTG

Basic information

species Glycine max
transcript GLYMA18G47420.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g01760.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcctctaaaacttcgtagtttgttgaacagagaggtagtatagtgtgttttggggtttggcttatctaaccttttgcgaggaatgccaaattatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCAAGTTGCGTCTGCATTGAGAATTGAAGTCAACCGGGGATTTGCTGTTTTG
                  |||   |  || |        ||||  |   |  ||||  || | | |||  |||  | ||  |   |||      | ||||   || |||||||||||||| |||||| ||||| ||||||| || ||||||||||| | ||    ||||||||| |||||  | ||| | || |||||||| |||
------------------gtaagcttctgcatt-----atagtg-acccttctttgatgtgtagtttagttaaattgttatgt--aattgtttttaatgt-atagGTCTCCACCTCGCATCCCGGAAGTTCATATTCCAGAAGATCCATTCCTGCAGGCTGTCAATGCATTGAGGATTGAGATTAACTGTGGTTTTGCTGTGTTG
















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|208031956|gb|GD829896.1|GD829896
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCC
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCC
EST: gi|298179899|gb|HO025114.1|HO025114
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|17963423|gb|BM270172.1|BM270172
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|21256005|gb|BQ452893.1|BQ452893
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTTTTTAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|208315190|gb|GE112664.1|GE112664
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGG
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGG
EST: gi|298176130|gb|HO015535.1|HO015535
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|298177074|gb|HO023435.1|HO023435
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|23057429|gb|BU578103.1|BU578103
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|298169425|gb|HO020785.1|HO020785
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|7926301|gb|AW832327.1|AW832327
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|11687897|gb|BF595573.1|BF595573
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATGCACAA                         ATCTCCAGCTCGCATTCCGGAATTTCATCTTGCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
EST: gi|298180408|gb|HO021961.1|HO021961
EST:     TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAA                         ATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA
genomic: TTGCTCGCAGTTCTGTTCTTGTGGTCCAATGCCCATACTTTCATCCACAAgtaagcctct ... tatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggggtttggcttatctaaccttttgcgaggaatgccaaattatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCAAGTTGCGTCTGCATTGAGAATTGAAGTCAACCGGGGATTTGCTGTTTTG
                 atctaac  putative branch site (score: 2)
                                         aaattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctctaaaacttcgtagtttgttgaacagagaggtagtatagtgtgttttggggtttggcttatctaaccttttgcgaggaatgccaaattatgttgcagATCTCCACCTCGCATTCCGGAATTTCATCTTCCAGAGGAGCCATTCCTGCAAGTTGCGTCTGCATTGAGAATTGAAGTCAACCGGGGATTTGCTGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT