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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGGATATGCTGTTGGAGCATTTAATGTATATAATTTGGAAGGAGTTGAGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaacagtcaggtcaaaatattgatttgtatgtatcccttttctttattgtgatagcacaaaaacgaggggagaaaagtggttgttggaaagccgc...

Basic information

species Glycine max
transcript GLYMA07G11610.1
intron # 32
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G11610.1 (Glycine max), 5'ss of exon 32
lower sequence: AT1G18270.1 (Arabidopsis thaliana), 5'ss of exon 36
GGGTGGATATGCTGTTGGAGCATTTAATGTATATAATTTGGAAGGAGTTGAGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcagg---------aacagtcaggtcaaaatattgatttgtatgtatcccttttc--tttattgtga-tagcacaaaaacgaggggagaaaagtggtt--gttggaaagccgc-------------------
 ||||||||||| |||||||||||||| || |||||  |||||||| | || ||||||||| | || |||||||||||| | |||||||||||||| ||||| ||          || |||    |    ||||  | | | |   |    ||  |  | | || ||| | |  |||| | |   |    |||| | ||   |     | |                      
AGGTGGATATGCAGTTGGAGCATTTAACGTGTATAACCTGGAAGGAATAGAAGCTGTTGTAGCGGCCGCAGAGGAAGAAAATAGTCCTGCTATATTGCAGgttagtgttctgaccaaaagtggatttctgatatacaatagcaaccaaagattaacattctgttctgagttgttcaaagatgtccgacacaaagagatttgataactgaactttttttggctaccttttttag

upper sequence: GLYMA07G11610.1 (Glycine max), 5'ss of exon 32
lower sequence: Vv17s0000g02140.t01 (Vitis vinifera), 5'ss of exon 34
GGGTGGATATGCTGTTGGAGCATTTAATGTATATAATTTGGAAGGAGTTGAGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaacagtcag--gtcaaaatattgat--ttgtatgtatcccttttctttattgtgatagca---caaaaacgaggggagaaaagtggttgttggaaagccgc
|||||||||||||||||||||||| ||||| |||||| |||||||||||||||| |||||  |||||||||||||||||||||||||||| || |||||||| || | |  |     ||||| | || ||   |  |  ||||    ||  |||||    ||| |    |||   | |||    |  |    || |           
GGGTGGATATGCTGTTGGAGCATTCAATGTTTATAATCTGGAAGGAGTTGAGGCAGTTGTTGCTGCTGCAGAGGAAGAACAAAGTCCTGCCATTTTACAGgttagaagctatggactgtcaagacatggacaatactcagtattaacttcttttataaatatatctatccaagttctaggccccagcaaaaattttccat-------
















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|298194330|gb|HO040978.1|HO040978
EST:     AGGCTGTTGTATCTGCTGCAGAGGAAGAACAGAGTCCTGCTATATTACAG                         ATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
genomic: AGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaaca ... acaatttcagATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
EST: gi|15813015|gb|BI785290.1|BI785290
EST:     AGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAG                         ATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
genomic: AGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaaca ... acaatttcagATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
EST: gi|13482034|gb|BG511377.1|BG511377
EST:     AGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAG                         ATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
genomic: AGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaaca ... acaatttcagATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
EST: gi|193315872|gb|FK281028.1|FK281028
EST:     AAGTCCTGCTATATTACAG                         ATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC
genomic: AAGTCCTGCTATATTACAGgtcaggaaca ... acaatttcagATCCATCCAGGTGCCTTGAAGCAAGGAGGAATTCCCTTGGTTGCTTGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTGGATATGCTGTTGGAGCATTTAATGTATATAATTTGGAAGGAGTTGAGGCTGTTGTATCTGCTGCAGAGGAAGAACAAAGTCCTGCTATATTACAGgtcaggaacagtcaggtcaaaatattgatttgtatgtatcccttttctttattgtgatagcacaaaaacgaggggagaaaagtggttgttggaaagccgc

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaga