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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttctagatctctagggttagggtattgcaatcaaaacaaaacaatttggttcactttagcttctatcgaaattgagtaaattacactgatccct...

Basic information

species Glycine max
transcript GLYMA18G47910.1
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 5'ss of exon 2
AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttctagatctctagggttagggtattgcaatcaaaacaaaacaatttggttcactttagcttctatcgaaattgagtaaattacactgatccct-----
|||||||||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||      |  || | |||  |||||    | | |     || ||   |  | | |   |||| || |   |     || | |   |||    |     
AAAATGGATATGGGACCATGCCCAAAGGTGCACTCTTTGCAGCTTCGGAAAGAgtatcctttgtttacagtaagttta--gtatttaccttatacggttaccatgaaggccgcct--acttccat-ggcctctttcaattgaatttgacatttgaaca

upper sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 5'ss of exon 2
AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttctagatctctagggttagggtattgcaa-tcaaaacaaaacaattt----ggttcactttagct--tctatcgaaattgagtaaattacactgatccct-------------------
|||||||||||||| || ||||| ||||| ||||| ||||||||  ||||||||||||||| |     |  | |   ||  | || |   |            ||||     || |||  ||| |  ||  | | |  | | |    | | ||  |   |                   
AAAATGGATATGGGTCCTTGCCCAAAGGTGCACTCTTTGCAGCTGAGGAAAGAgtatcctttttttaatgaatgtaaagtctttttcttcttcgtgtgttgttatttctaaagtccacactagttattcagtaggatgttatttcgctcctctactgttttgctttaactcgtctttag

upper sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 2
AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttctagatctctagggttagggtattgcaatcaaaacaaaacaatttggttcactttagcttctatcgaaattgagtaaattacactgatccct---
|||||||||||||| || || || ||||| ||||||||||||||  |||||||||||||||      || | | | || |  ||| ||               ||  | |   ||||   | |||   | |        |||     || | |   
AAAATGGATATGGGGCCATGTCCGAAGGTGCACTCCTTGCAGCTAAGGAAAGAgtatcctttcgccactatggtgctatg-catttcagcttttcttctttctttaagatg--tttaaactgtatgatactctttactgttagggccatgcgttct

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|192296271|gb|FG989063.1|FG989063
EST:     ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|208271764|gb|GE068686.1|GE068686
EST:     GGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: GGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|193555503|gb|FK515948.1|FK515948
EST:     ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|209725035|gb|BW659770.1|BW659770
EST:     ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|193492617|gb|FK455741.1|FK455741
EST:     ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|193649862|gb|FK595459.1|FK595459
EST:     ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
EST: gi|208276609|gb|GE074791.1|GE074791
EST:     ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA                         ATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA
genomic: ATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttct ... ctgtttctagATATGAGGAGGCGAAAGCAAAGGGGACCGATAATTATGACAGGGAGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGAgtatccttctagatctctagggttagggtattgcaatcaaaacaaaacaatttggttcactttagcttctatcgaaattgagtaaattacactgatccct

- - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaaa