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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcccacttaagtgacaattagtttgaaggtgtagtattgtttcttaaacatctctcatatagaaggcaaatatttgatgcttgattgtgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAA

Basic information

species Glycine max
transcript GLYMA18G53700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------------------------------------------------aatgcccacttaagtgacaattagtttgaa--ggtgtagtattgtttcttaaacatctctcatatagaaggcaaatatttgatgcttgattgtgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAA-
                                                                                               | |       |||| ||| ||  | | |   ||  ||| |        |  |  || |   | | |  || |||  | ||||  ||   | |  |  | |||  | |  || ||     | | ||| ||||||| | ||| |||||| ||    ||||||||||| |||||||| ||||| |||||||| ||||||||||| 
gtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacattttttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgatttttttgtttaatt-tgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT

upper sequence: GLYMA18G53700.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 1
aatgcccacttaagtgacaattagtttgaaggtgtagtattgtttcttaaacatctctcatatagaaggcaaatatttgatgcttgattgtgttcatt-caGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAA-
  |      || | |      || ||  || || || | ||          |     |  || ||   |  ||  | | || |   ||  | || ||| |||  ||| ||| ||||||   || || |||||||| |    |||||| |||   ||||||||||| |||||| | | ||||||||| |||||||||||||| 
--ttgttgtttcatttttctctaattctaaagtttaatttttaaaggctttctctgattgtaaagtttgagaagttctcattccgtatgttatttattacagTGTCAGATGTTCCCAACTTGAGGGAAATGGAAGCCAAATAAAGAGAACAACTCTTCATGATCTCTATGAGCAGGGAGGGCAGAGCCCATGGTATGATAAC
















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|209706284|gb|BW680671.1|BW680671
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|7233907|gb|AW569249.1|AW569249
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|6566822|gb|AW234454.1|AW234454
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|213592579|gb|DB961839.1|DB961839
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|213593697|gb|DB971719.1|DB971719
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|7233788|gb|AW569131.1|AW569131
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|21887135|gb|BQ740348.1|BQ740348
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|254318817|gb|GR830381.1|GR830381
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|6913943|gb|AW395473.1|AW395473
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|18721154|gb|BM523327.1|BM523327
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|298174178|gb|HO017514.1|HO017514
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|7924409|gb|AW830435.1|AW830435
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|192317350|gb|FK010581.1|FK010581
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|24136489|gb|BU926999.1|BU926999
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
EST: gi|24205422|gb|BU964675.1|BU964675
EST:     ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTAC                         GGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG
genomic: ATCCGCTTCCCTCCGATCCATTCACTCGCTCCCTCTTAAAACCTCCTTACggtaagtttt ... tgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaacatctctcatatagaaggcaaatatttgatgcttgattgtgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAA
                                    gcttgat  putative branch site (score: 5)
                                               ttcattc  putative PPT
                         aaatatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcccacttaagtgacaattagtttgaaggtgtagtattgtttcttaaacatctctcatatagaaggcaaatatttgatgcttgattgtgttcattcaGGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- tgcccac
- - - - - - - - - - - - - - - ggtgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct