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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattatttatttataaagtagctagaacatccctttcggatttaaaaagaaaattttgttttattaaactaattttgtctcgtttgtttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG

Basic information

species Glycine max
transcript GLYMA05G08590.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G08590.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G01500.1 (Arabidopsis thaliana), 3'ss of exon 4
--gaattatttattta--taaagtagctagaacatccctttcggatttaaaaagaaaattttgttttattaaac--taatt--ttgtctcgtttgtttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG
   |||||   ||  |  |||        | | |||    | |  | ||||   |||||      |||  |||   |||||         || ||  || |  | |||| ||||||||||||||| ||||||||| | ||||| ||||| || || || || || || |||||||| ||||| |||||| | ||  | |||||||| |
gtaaattaaaaataaaactaatactatgtgtatatcatggttgcttataaattaaaaatgaaacattaagaaaaagtaattaacaaaggtgtgtgaatggtggtgcagTACATGGTGTTTGCTTGTTCAGACTCACGTGTGTGTCCATCACACGTTCTGGACTTTCAGCCAGGAGATGCCTTCGTGGTCCGTAACATAGCCAACATGG

upper sequence: GLYMA05G08590.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G14740.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------gaattatttatttataaagtagct-----agaacatccctttcgg-atttaaaaagaaaattttgttttattaaactaattttgtctcgtt-tgt----ttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG
                |  |   || ||||||| || |     | || ||   | ||   || | || |    |  || || | ||  ||| || || | | ||  | |    |   || | |||| ||||||||||||||| || |||||| | ||||||||||| || || ||||| ||||| || ||||| ||||| |||||  | ||| | ||||| || |
gtaaaacaaaaataagaagaaaaatatataaagcagttgatgaaaaatatagttatctctatatgaatatgttagatttttcttttggactcatattatatggtcatatactatgaattgtgcagTACATGGTGTTTGCTTGTTCGGACTCACGAGTGTGCCCATCACACGTACTAGACTTCCATCCTGGAGATGCCTTCGTGGTTCGTAATATCGCCAATATGG

upper sequence: GLYMA05G08590.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01210.t01 (Vitis vinifera), 3'ss of exon 4
----gaattatttatttataaagtagctagaacatccctttcggatttaaaaagaaaatttt----gttttattaaactaattttgtctcgtttgtttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG
      |   || |||| || | |         |  | |||| |  | |  |  |||||||      |   | |  |||| ||   |  |      ||  | || |||||||||||||| || ||||| |||||  |||| |||||||| |||||||| || ||||||||||| || || ||||||||| | || ||||||||||| |
aaacagacccttaatttctacatt--------tacgcgtttcaggatgagtagaaaaatttacaaaatgacagttgactagttaattaactacaaatttatgttgcagTTCATGGTGTTCGCATGCTCGGACTCTCGGGTTTGCCCATCACATGTGCTGGACTTCCAACCAGGGGATGCTTTTGTGGTCCGGAACGTTGCCAACATGG

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|20813335|gb|BQ297813.1|BQ297813
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|9204696|gb|BE330920.1|BE330920
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|13480423|gb|BG509766.1|BG509766
EST:     AAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: AAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|17401473|gb|BM178255.1|BM178255
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|17519330|gb|BM188372.1|BM188372
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|6724386|gb|AW308785.1|AW308785
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|9902528|gb|BE611496.1|BE611496
EST:     ACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: ACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|10234895|gb|BE803783.1|BE803783
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|20813172|gb|BQ297650.1|BQ297650
EST:     TGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: TGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|20813221|gb|BQ297699.1|BQ297699
EST:     GCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: GCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|10845384|gb|BF068521.1|BF068521
EST:     GGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: GGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|27425773|gb|CA937293.1|CA937293
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|10846842|gb|BF069578.1|BF069578
EST:     GGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: GGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|17400472|gb|BM177254.1|BM177254
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|11412390|gb|BF424401.1|BF424401
EST:     AAGAATCCACCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: AAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|6134539|gb|AW132932.1|AW132932
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTTAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|17519040|gb|BM188082.1|BM188082
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|17152932|gb|BM142865.1|BM142865
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|20812505|gb|BQ296983.1|BQ296983
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|7326620|gb|AW620418.1|AW620418
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|6134971|gb|AW133364.1|AW133364
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|9900268|gb|BE609236.1|BE609236
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|22525380|gb|BU084191.1|BU084191
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|7639455|gb|AW733777.1|AW733777
EST:     AACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: AACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|22525231|gb|BU084042.1|BU084042
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|17401464|gb|BM178246.1|BM178246
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTTATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|20812735|gb|BQ297213.1|BQ297213
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|7640317|gb|AW734621.1|AW734621
EST:     CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: CAAGAATCCAGCTTTGTATGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
EST: gi|6914576|gb|AW396106.1|AW396106
EST:     TGGTGAACTTGCCAAAGGCCAGAGCCCCAAG                         TTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA
genomic: TGGTGAACTTGCCAAAGGCCAGAGCCCCAAGgtatttattc ... gttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagaaaattttgttttattaaactaattttgtctcgtttgtttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG
                      aactaat  putative branch site (score: 2)
                                      tttgtttgttttttc  putative PPT
     aaaattttgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattatttatttataaagtagctagaacatccctttcggatttaaaaagaaaattttgttttattaaactaattttgtctcgtttgtttgttttttcagTTCATGGTGTTTGCTTGCTCAGACTCAAGGGTGTGCCCATCTCATGTGCTAGATTTCCAACCAGGAGAGGCCTTTGTGGTCAGAAATGTTGCCAACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG