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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttttcatcctaaacgatagattgaagttactgtttgcatatgatttgtcttgacttttttgcctttaattttaattcttttcctgctcattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGAG

Basic information

species Glycine max
transcript GLYMA05G03730.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g41460.8 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------------------------------gtt-ttttcatcctaaacgatagattgaagttactgtttgca-tatgatttgtcttgactt--ttttgcctttaattttaattcttttcctgctcattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGAG
                                                                                       ||  ||||   | |  | ||   ||     ||  | || ||| | |  ||| | |  |||   |  ||  ||||  | ||||     |   |    ||||  || ||||||||||| |||||| |||| || ||||||||||||||||| || |||
gtgagaatcatatgacatgatgtcagagatacattttttttttgcattacgccatgtttaatatattttttcttgactagatttatggtcatttttcacttcgatgaagaatcattattgtttttggcagttttgtttatgtgtactaaatactgtgtttatatctaatctagatttcgtc--ttcac-agATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG
















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|209698686|gb|BW656511.1|BW656511
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|31462360|gb|CD404388.1|CD404388
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|209729083|gb|BW655073.1|BW655073
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTG
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTG
EST: gi|6455321|gb|AW186004.1|AW186004
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|120496159|gb|EH224326.1|EH224326
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|13482176|gb|BG511519.1|BG511519
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|209729478|gb|BW655108.1|BW655108
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|10254275|gb|BE822041.1|BE822041
EST:     GCTACTGTGATTGCATTAGGATT                         GTTCTTCNNNCTTGATGATCTGACNNNATTTGAGATCACATATCTACTAGA
genomic: GCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|209698687|gb|BW656512.1|BW656512
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
EST: gi|13482252|gb|BG511595.1|BG511595
EST:     TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATT                         GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA
genomic: TTAAAGATGTTGCTGCTGAACGTCCCGGCTACTGTGATTGCATTAGGATTgtaagtagtt ... cattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtcttgacttttttgcctttaattttaattcttttcctgctcattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGAG
                          ttttaat  putative branch site (score: 3)
                                ttcttttcctgctcat  CT-rich tract
            ttttttgcctttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttcatcctaaacgatagattgaagttactgtttgcatatgatttgtcttgacttttttgcctttaattttaattcttttcctgctcattcattagGTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - gttactg
- - - - - - - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgcc