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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggttatttacagttaaacttagcctttgttgctactattttttcaactcaatgtagttttccatcagcgtgttttcttgcattttgattaatataaccttttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCATGGGTCAAACTCTACAGAGCGAG

Basic information

species Glycine max
transcript GLYMA06G05900.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 22
-----------------------------------------gttaggttatttacagttaaacttagcctttgttgctactatttttt-caactcaatgtagttttccatcagcgtgttttcttgcatttt-gattaatataaccttttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCATGGGTCAAACTCTACAGAGCGAG
                                           ||||  |   | | | ||| ||   ||||| ||   | || |    |   |   | |    ||   |     |  ||| |   | |||  | | || |||||||||   |||||||| |||||||||||||||||||||||| |||||||   ||   | ||||||  | |  |  | ||||||||||
gttaaaagatttttgctgtatttttttaatccctttgttttactaggcca--gaaactcaaagttgtgctttgctgtgtcaatataaaactggttgttttgaccttgtttttttttcctttttcaaactttcaactgatgtaacctttttcatgcagTTTCATTGGAAATCCTGGTCTTTGTGGTTATTGGCTTAGTTCTCCATGTCATCAGGCTCATCCAACAGAGCGAG
















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|208308475|gb|GE103687.1|GE103687
EST:     GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAG                         TTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
genomic: GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAGgttaggttat ... ttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
EST: gi|192296635|gb|FG991203.1|FG991203
EST:     GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAG                         TTTTATTGGAA-TCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
genomic: GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAGgttaggttat ... ttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
EST: gi|207838799|gb|GD810461.1|GD810461
EST:     GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAG                         TTTCATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
genomic: GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAGgttaggttat ... ttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
EST: gi|193405997|gb|FK370854.1|FK370854
EST:     GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGG-TTTCCCCTGACAG                         TTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
genomic: GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAGgttaggttat ... ttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
EST: gi|193431703|gb|FK395209.1|FK395209
EST:     GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAG                         TTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
genomic: GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAGgttaggttat ... ttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCA
EST: gi|193342439|gb|FK306083.1|FK306083
EST:     GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAG                         TTTTATTGGAAATCCTGGTCTTTGTGGTGAATTAGGCTGGATTTGTCTTGT
genomic: GTTGGTGTTATTCCCACAAGCAAGAATTTTTCCAGGTTTTCCCCTGACAGgttaggttat ... ttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGA-TT-GGCTGGATTTGTCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttccatcagcgtgttttcttgcattttgattaatataaccttttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCATGGGTCAAACTCTACAGAGCGAG
                                   atataac  putative branch site (score: 3)
                                         ccttttat  CT-rich tract
                         attttgattaatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggttatttacagttaaacttagcctttgttgctactattttttcaactcaatgtagttttccatcagcgtgttttcttgcattttgattaatataaccttttatgtgcagTTTTATTGGAAATCCTGGTCTTTGTGGTGATTGGCTGGATTTGTCTTGTCATGGGTCAAACTCTACAGAGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA