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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA

Basic information

species Glycine max
transcript GLYMA01G40650.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 5
aattgacaacccattattccttttccttttatgctacaagtattc-aaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
   |   ||  |  || | ||||   ||  |||  |   |  | |  ||  | | |  ||    ||| |  || |  ||||   ||  || ||   ||||||  ||  || |||||||||||||||||||||||||| | ||||| || |   | || || |  || || || || ||||||||  ||||| |  | || |
--gtatgaattc--tactgctttcagttcgatggaaatggagtcctgaatttgggatatttgcgctgat--cttaactgtg--ctgattgatatg-tgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA

upper sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G17840.1 (Arabidopsis thaliana), 3'ss of exon 5
-aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
  |||    |     | |||   |||||| | | || |  ||      | || |   ||| | |   ||   | |||| | ||| || ||  ||  |  |||| ||  |  |||| |||||||| ||||||||||||| |||||| ||   | ||||||| |  || |||||||||||||| ||||| ||||| || ||||
gtattatagattttctgttc---ttccttgtctccttcttgttccttgaactcg---tttaagt---gtatttgacttttaatt-gtttg--aattttcagACTGGACTCTTGCCACCATTTGTACCATTTGCTCAAGTATTTGCAGCCACTATTACAGCCGCTCTCACTGGTTCTCTCTACTACATAGCTGCTTCCCCTA

upper sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 5
aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
             | |   ||  | | ||   | | |      |||   | |     || ||        || ||| |||| || |     ||| ||||||| || ||||||||||||||||| |||||||| || || ||||| |||||  | |||||||  ||||||||||| ||||||||  ||||||||||||| |
------------gtaagagctccttcctt--ggtttcggactgtcatgacaactgaatttat------atcttact-gtgaattctt---caaattgtagACTGGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAA

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|23732337|gb|BU764328.1|BU764328
EST:     TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTG                         ACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
genomic: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTGgtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
EST: gi|192317383|gb|FK007505.1|FK007505
EST:     TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTG                         ACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
genomic: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTGgtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
EST: gi|7693502|gb|AW761594.1|AW761594
EST:     TTTACGAGGCAGTAATCTTATAACAGATGTTCAATGAATGGCATCATTTG                         ACCG-TGTGCTGGCTCCATTTGGTTC-ATTTGCT
genomic: TTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATT-Ggtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTG-TTCCATTTGCT
EST: gi|151400500|gb|EV270314.1|EV270314
EST:     TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTG                         ACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
genomic: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTGgtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
EST: gi|11274513|gb|BF324866.1|BF324866
EST:     TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTG                         ACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
genomic: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTGgtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
                       gactaac  putative branch site (score: 1)
                                             taaaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - -acaaccc
- - - - - - - - - - - - - - - -tgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgg