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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCACCTGCAGAGTTGCGATTGCGCTCTTTCCAGATCTCGTAGATTCCGCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattccttcgttcttttgttttttctctttcgcaattcgatctgctctctgctgtgattttgttttgcgtttaactcttcctttatttgccattgctg...

Basic information

species Glycine max
transcript GLYMA12G04820.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 1
--GAGGCACCTGCAGAGTTGCGATTGCGCTCTTTCCAGATCTCGTAGATTCCGCACATGGCTCAGCCGCTCGT---GAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt-cgttcttttgttttttctctttcgcaattcgatctgctctctgctgtgattttgttttgcgtttaactcttcctttatttgccattgctg
    ||| ||  |      |||  ||||    | | | |    | || | | || |||||| |||||||||||   |||||||||||| |||| |||||| ||||||||   ||  ||       |  | |  ||| || |  |||| ||   ||  |||     | | |   | |  ||   | | ||  |   |||    |   
CTCGGGCGCCCTCTCGCGCGCGCGTGCGTCGCTCCGACA----GCAGCTGCAGC-CATGGCGCAGCCGCTCGTCGTGAAGAAGGACGACGACCTCGACGAGGAAGgtgagcgctcgcgcgtcagcgcctctcgtctgtcccgcttcgttcc-ttcgttgcgcccgtgtgggcctccagttgtgtgtgcccgtgcgtgcgtgcgtgt

upper sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 1
GAGGCACCTGCAGAGTTGCGATTGC-GCTCTTTCCAGATCTCGTAGATTCCGCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattccttcgttcttttgttttttctctttcgcaattcgatctgctct-ctgctgtgattttgttttgcgtttaactcttcctttatttgccattgctg--
|  |    | |    ||    |  | | |||     | || |    ||||| | |||||||||||| ||||||||||||||||| || |||||||| |||||||  | |     | | || |||||  | |||   ||||||||    |    || |   |  || || |    | || |  |     |   | |  |   |  
GCTGTGTTTCCTTCCTTTTCTTCCCAGATCTGAATCGGTCCCTCTCATTCCAC-CATGGCTCAGCCTCTCGTGAAGAAGGACGACGATCGCGACGATGAAGgtgtgttcgaaaatttattttttttattttttttaaattcgattcaattgattgatccaaactttttcta---tcaatttctgtagaagaagtcggtcaagcg
















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|207809660|gb|GD782336.1|GD782336
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTT-GGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|208253489|gb|GE054277.1|GE054277
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|213620091|gb|DB965397.1|DB965397
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|209696738|gb|BW660435.1|BW660435
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|208317000|gb|GE111469.1|GE111469
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|209720618|gb|BW677326.1|BW677326
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|209703331|gb|BW683311.1|BW683311
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
EST: gi|207679964|gb|GD664418.1|GD664418
EST:     GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAG                         CTGAGTATTCTCCCTTTT-GGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG
genomic: GCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattcctt ... tggttaacagCTGAGTATTCTCCCTTTTTGGGAATTGAAAAGGGAGCTGTTCTTCAGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCACCTGCAGAGTTGCGATTGCGCTCTTTCCAGATCTCGTAGATTCCGCACATGGCTCAGCCGCTCGTGAAGAAGGACGATGACCGCGACGACGAAGgtgattccttcgttcttttgttttttctctttcgcaattcgatctgctctctgctgtgattttgttttgcgtttaactcttcctttatttgccattgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcttcc