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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaatcattgacagaaagagtagtatccattttgacattaatcttttgtaattgtccttgtcattattttatttgttctcctgtgacatgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG

Basic information

species Glycine max
transcript GLYMA19G08050.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G862959_T04 (Zea mays), 3'ss of exon 6
tgtaatcattgacagaaagagta--gtatccattttgacattaatcttt-tgtaattgtccttgtcattattttatttgttctcctgtgacatgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
  | | |||  |||   | | |   || | | | ||    ||    | | ||| |   || |  |     | | | |  ||      |||      |   ||| | ||||||||| ||||| |||||||||||||| ||||| |||| |   |||| 
-attaccatgtacatgcacattttcgtgtgcctgttactgttgccttatatgtgaccatcatcctgtaagtatcactcatttaatattgatgcacgt--gcagGTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACT---CAAAA

upper sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
tgtaatcattgacagaaaga-gtagtatccattttgacattaatcttttgtaattgtccttgtcattattttatttgttctcctgtgaca---tgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
  |||  | ||  ||| ||  ||  |  |    ||    | ||| | |||   ||       |   ||| |   |     |   ||  ||   |  ||| ||||| |||||||||| ||||| |||||||| |||||||||||| |  ||||||| ||
--taa--actggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagattcatatatgggtctaaataaagtttcaaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG

upper sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------tgtaatcattgacagaaagagtagtatccatt-ttgacatta-atcttttgtaattgtccttgtcatt-------attttatttgttctcctgtgacatgatttga----------cagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
                                                                  | | ||  || |      ||    |||   ||  || ||  | |        | |||| ||||| |           || || | |    ||   | ||| ||  |          |||| |||||||||| ||||| |||||||| |||||||||||| | || || || ||
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatcta-aatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG

upper sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
-tgtaatcattgacagaaagagtagt-atccattttgacattaatcttttgtaattgtccttgtcattattttatttgttctcctgtgaca--tgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
   |  |   | ||||   || |  |  | |  ||| | |  |||      ||  || |||||| ||| ||  ||   |  |  ||  |||  |   |   ||||||||||||||| ||||||||||| |||||||||||||| || |||||||||||
aacttttttataacagtgcgattgattgtgccctttaataa-aattcagcatacatg-ccttgt-attgttc-ataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG

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|6455745|gb|AW186428.1|AW186428
EST:     GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
EST: gi|151403633|gb|EV273443.1|EV273443
EST:     GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
EST: gi|193408580|gb|FK370344.1|FK370344
EST:     GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
EST: gi|193341998|gb|FK308960.1|FK308960
EST:     GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
EST: gi|193400938|gb|FK365387.1|FK365387
EST:     GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
EST: gi|193350382|gb|FK316224.1|FK316224
EST:     GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGA                         ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA
genomic: GATGAATGGTTTGTCGTAAAAGTGATTCATTTTGATAAGGAATCAAAGGAgtaagtatac ... gatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaattgtccttgtcattattttatttgttctcctgtgacatgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
             ttgtcattattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaatcattgacagaaagagtagtatccattttgacattaatcttttgtaattgtccttgtcattattttatttgttctcctgtgacatgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA