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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGGCATCAGGGCTTGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaatttttaattaagtactgtgctgtaataagctaattttctgggaaagttatgttaaaatatgtacttttggctggaaaaagtatcccaagcttgag...

Basic information

species Glycine max
transcript GLYMA01G36890.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 4
AACTGGCATCAGGGCTTGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgta---aatttttaattaagtactgtgctgtaataagctaattttctgggaaagttatgttaaaatatgtacttt-tggctggaaaaagtatcccaagcttgag
| || || |||||  |||| |||||  | |||||||||||||| |||||||||   || |||||||||||||||||||| ||||    |||  | ||||||||   || || |   |  || |  |  ||  || |  |  || |      || |   |  |  | ||  | ||| |  ||| |  |    |      ||    
AGCTAGCCTCAGGCATTGCCGAGGTAGTGAAGTATGGGCTCATAAGGGATGCACCATTCTTTGAGTGGCAAGAGAAAAACATGCCTGAATTGTTAGCAAGgtactcaacttgttcctgtgtgcattaatgctatcatatttttattctacgaattgtagacactagatacagtttataactgtattagacttgtggtcct----

upper sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G051129_T01 (Zea mays), 5'ss of exon 3
AACTGGCATCAGGGCTTGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaatttttaattaagtactgtgctgtaataa-gctaat---tttctgggaaagttatgttaaaatatgtacttttggctggaaaaagtatcccaagcttgag----
| || || |||||  |||| |||||  |||||||||||||||| |||||||||   || ||||||||||||||||| || ||||    |||  | ||||||||    || || |   | ||||| || | | | ||||     ||| ||   ||    |  || ||  |  ||    |  |   | || | |   |  |||| |    
AGCTAGCTTCAGGCATTGCCGAGGTAGTAAAGTATGGGCTCATAAGGGATGCACCATTCTTTGAGTGGCAAGAGAAGAACATGCCGAAATTGTTAGCAAGgta----ttcaacttgtttctgtg-tgcactgatgctatcgtatttttgttcaacgagttgtagaacctacacagcagttt---ataactgtattagacttgtggttc

upper sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 4
AACTGGCATCAGGGCTTGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaatttttaattaagtactgtgctgtaataagctaattttctgggaaagttatgttaaaatatgtacttttggctggaaaa--agtatcccaagcttgag---------
|  ||||||||||  |||| |||||||| ||||||||||| ||||||||||| || || ||||||||||||||||| ||||||||   |||| |||||||||||        | || || |    | | || |  |  || |     ||| ||   ||    |||||    || |||   |    | ||    |   |||           
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaa--------taaaatattccattctcatcatattcttcttaaaaaaaatttgattt---tatgtgagattagcttatagttcaatacttaagatttgcattcagtgat

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|22932048|gb|BU549187.1|BU549187
EST:     AGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAG                         AGATNNTAGTGCAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: AGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGCAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
EST: gi|208303624|gb|GE101369.1|GE101369
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAG                         AGATCCTAGTGCAATGGCATATG
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGCAATGGCATATG
EST: gi|298196729|gb|HO041472.1|HO041472
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAG                         AGATCCTAGTGCAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGCAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
EST: gi|192333520|gb|FK024049.1|FK024049
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAG                         AGATCCTAGTGCAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGCAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGGCATCAGGGCTTGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaatttttaattaagtactgtgctgtaataagctaattttctgggaaagttatgttaaaatatgtacttttggctggaaaaagtatcccaagcttgag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaag