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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG

Basic information

species Glycine max
transcript GLYMA15G04500.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG
||| |||  ||||| | |     || |||   ||     | |  |  ||   | ||  |  ||  | ||  |  |  |  || || | ||          |||| | | |  |  ||||||| ||| | ||||| ||||||||||| || || || |||||||| ||||||||||| || || | ||||||||| ||||
gtaaatttgttcatctga-----aatttg---aaatttatttgctttgg--tttttcataaattatctttcaagttctcttacagtttta---------tttaacttttt--ttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG
                            |   || | |||||    ||    || ||||  |   || | | | | | |||  | ||     || |  ||||   |     || ||   ||| ||| | || || |||||||| || || || || |||||||| ||||||||||| ||||| ||||| ||||||||||
------------------------gtaggagtaaacacttat---cagcttttaattctcaa--cttatctgcgtgtcaattcacatt----cttataacttggtttct--attatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG
                 | | | |   | ||    |  ||| |||     ||   |  ||     || |    ||     | |  |     ||||| ||  ||     |    | |  |||| || || || ||||||||||||||||| || ||||||||||| |||||||||||||| |||||||| ||||| || |
--------------aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaat-----ttagcaccctcactgaaga--tagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttataca----tattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG
||| || |     |  | ||     |||| |  | |  | |   |  |   |  |||||| |   |  || |||    |  ||   || || |   || |  || |   |   ||        ||||||  | || |||||||| ||||| || || || ||||||||  | |||||||| |||||||||||||||||  |||
gtaaatccaac--tcacgttacacgcttggtgcacca-tcacgctctgtg-cagtttctgaactctgatacacaatcattctacacaaaatattacctta--acgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG

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|213611728|gb|DB962965.1|DB962965
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAG
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAG
EST: gi|151412093|gb|EV281905.1|EV281905
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
EST: gi|192316740|gb|FK006443.1|FK006443
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGCTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
EST: gi|213591579|gb|DB955787.1|DB955787
EST:     CTTGTGCATCCCCAACCCTGAA-GTTATTGGGGCAATGTTAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: CTTGTGCATCCCCAACC-TGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
EST: gi|192316741|gb|FK006444.1|FK006444
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGCTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
EST: gi|16279667|gb|BI943554.1|BI943554
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGGTAACCCTATTG                         GAGGTTCGTA-TTGCTATGATGAGGGGAA
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAG-TTCGTAGTTGCTATGATGAGGGGAA
EST: gi|192317198|gb|FK007909.1|FK007909
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
EST: gi|19453064|gb|BM954474.1|BM954474
EST:     TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
EST: gi|192296657|gb|FG991225.1|FG991225
EST:     TCTTGTGCATCCC-AACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG                         GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT
genomic: TCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTGgtagattcct ... ataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG
        tattaat  putative branch site (score: 2)
                                acttaaatatatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA