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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgctcaattcaataccatatgcatttgtgggtggtagctgacttaggatagataccatgttttttatcactaactgagaactggcgttgcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAGAGGTCTGGTTAGAACAGATGAAAGCAAACAGAACATTGGTGCTGCAGAT

Basic information

species Glycine max
transcript GLYMA18G39930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G39930.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 1
aatgctcaattcaataccatatgcatttgtgggtggtagctgacttaggatagataccatgttttttatcactaactgagaactggcgtt---gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAGAGGTCTGGTTAGAACAGATGAAAGCAAACAGAACATTGGTGCTGCAGAT
 |  |||  |  ||   || |||  |  |       |  |     |    | ||       |||||||    |   ||| |  |  || |     |||||||| ||||||||||| || ||||| || |||||| || |||| | ||| || |||||| |||| |||||||| || |||||  |||| ||||| |  || || 
-actctctttgtaagtgcaaatgggtgggaaatatcttacccttctctctttgaccaagaattttttaat-ttggttgatatttatcggttaaaattttcagGCCAAATAGTTTATAAGAAATTGAAGGAGAGGGCAGACCAGTTTGTTGCCAGAGGTTTGGTCAGAACAGAGGAGAGCAAGGAGAAAATTGGAGGAGCCGA-
















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|207790818|gb|GD759603.1|GD759603
EST:     GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAC-AAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208266217|gb|GE065434.1|GE065434
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208030116|gb|GD831598.1|GD831598
EST:     AAGAGTACTGTGCTTGTTACGGGAGCGGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAGAGAGAGGCCAAACCAATATGTGGCTAG
genomic: AAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|213620500|gb|DB957344.1|DB957344
EST:     GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208169818|gb|GD973099.1|GD973099
EST:     G-GTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTA
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTT-ACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTA
EST: gi|208300259|gb|GE097294.1|GE097294
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAC
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTAC
EST: gi|208282481|gb|GE076911.1|GE076911
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAC-AAAAATT-AAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208164195|gb|GD962407.1|GD962407
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|193340963|gb|FK306344.1|FK306344
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAC-AAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|151397652|gb|EV267525.1|EV267525
EST:     GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAACCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208250912|gb|GE047291.1|GE047291
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAC-AAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208333442|gb|GE126207.1|GE126207
EST:     AAGAGTACTGTGCTTGTTACGGGAGCGGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAGAGAGAGGCCAAACCAATATGTGGCTAG
genomic: AAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|17023106|gb|BM094140.1|BM094140
EST:     GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|193318902|gb|FK283414.1|FK283414
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|298174286|gb|HO017622.1|HO017622
EST:     GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208085081|gb|GD883183.1|GD883183
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|193526092|gb|FK481541.1|FK481541
EST:     GTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|193577933|gb|FK533779.1|FK533779
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTT
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTT
EST: gi|192327079|gb|FK015471.1|FK015471
EST:     GTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|58016336|gb|CX703078.1|CX703078
EST:     GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208162540|gb|GD964755.1|GD964755
EST:     GTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|208146997|gb|GD950614.1|GD950614
EST:     AAGAGTACTGTGCTTGTTACGGGAGCGGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAGAGAGAGGCCAAACCAATATGTGGCTAG
genomic: AAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|193321356|gb|FK283658.1|FK283658
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTAC-AAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|58019388|gb|CX706130.1|CX706130
EST:     TGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: TGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
EST: gi|193450072|gb|FK415608.1|FK415608
EST:     GGGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGG                         ACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG
genomic: GAGTCTGAGAAGAGTACTGTGCTTGTTACGGGAGCCGGTGGTCGCACAGGttaggccttt ... gcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggatagataccatgttttttatcactaactgagaactggcgttgcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAGAGGTCTGGTTAGAACAGATGAAAGCAAACAGAACATTGGTGCTGCAGAT
                        cactaac  putative branch site (score: 1)
                                           ttgcttttc  putative PPT
                ttttttatcactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgctcaattcaataccatatgcatttgtgggtggtagctgacttaggatagataccatgttttttatcactaactgagaactggcgttgcttttcaggACAAATAGTTTACAAAAAATTAAAAGAGAGGCCAAACCAATATGTGGCTAGAGGTCTGGTTAGAACAGATGAAAGCAAACAGAACATTGGTGCTGCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
aatgctc
- - - - - -caatacc
- - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - gggtggt
- - - - - - - - - - - - - - - - - - - gctgact
- - - - - - - - - - - - - - - - - - - - - - - - - - - taccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaactg