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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctaagctgtctagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatttgaaatatttgagagctaaaattttgcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG

Basic information

species Glycine max
transcript GLYMA04G12950.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G800734_T02 (Zea mays), 3'ss of exon 5
--tgctaagctgtctagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatttgaaatatttgagagctaaaattttg--cacatg-tagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG
  |  | |       | | |   | || | |    |||     || | | ||   |||       |||  ||   |    |  || ||||  |   |||    |||| ||||| || ||  |||  | ||| || |||||||||||||||||| | |||||||||   ||||| |||||||| ||||| |||||||||
tttttttaataaaacaatcaatcttttat-atgcccagatgccctttaaatgc--ttgtactccttttttaaggct--gcatttacaattccggtaacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCCGAGGGAAGACGGGCTTTACATTTTGCATGTGGCTATGGTGAG

upper sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
lower sequence: AC215244.3_FGT002 (Zea mays), 3'ss of exon 5
-----tgctaagctgtctagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatttgaaatatttgagagctaaaattttgcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG
        | | ||||||  | |  |||     |  | |  || | |     | ||  |||  | |||| ||      |||    ||||||||     ||  |||||  | || || |||||||  | ||| || ||||||||||||||||| || ||||||||||  || || |||||||| ||||| || ||||||
aacatcatttatctgtct--tcacagtaaatacagttgccaccttgcctactgggtt-ttgattttgatatgctgacgttgtcttctaaaattc-atgca-atagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG

upper sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G35450.5 (Arabidopsis thaliana), 3'ss of exon 6
----------------tgctaagctgtctagttatggtattgttaaattcagccattctc------ttag-tgtcattgggtatgatttgaaatatttgagagctaaaattttgcacatg-------tagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG
                 | |||  ||  |    |||  |   |||  ||  |   | ||       |||| |||     | | || ||||    | | |  |  |  | ||||   | |        ||||| ||||||  |||  | ||  |||||| | |||| |||||||||||||| || ||||| || || ||||||||||| |||||||| || |||
gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcgtta-ttggatttttattcgttgattcattagGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG

upper sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------tgctaagctgtctagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatt------tgaaatatttgagagctaaaattttgcac-atgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG
                  || ||  || ||  |||   |      || |||      ||   |  |  ||||||     | ||      | || | | || |   | |  |  || || |   |||| ||||||  |||  | ||  ||||||   |||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| || |||
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG

upper sequence: GLYMA04G12950.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 3'ss of exon 6
tgctaagctgtc--tagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatttgaaatatttgagagctaaaat---tttgcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG
   ||  || |   || | |     |   || |||  |  ||  | ||||| || ||       ||| | ||  ||  |    |  | |   |||| | || ||||| ||||| |||||||| ||| ||||||| ||||| ||||||||||||||||||||||| |||||  ||||||| || ||||| |||||||||
--ttattctattaataatgacaaagtgaatatattttgt-atctttttagt-tcgtttttagcaattagcaaggttgaaagtttccactctatttgtaaat-tagGGTTTGAAGAATGCACTTGCCTCTGGTGCCGACAAAGATGAAGAAGATTCAGAGGGAAGGACTGCACTGCATTTCGCATGTGGGTATGGTGAG

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|31457503|gb|CD399531.1|CD399531
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|192324548|gb|FK018704.1|FK018704
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|16996353|gb|BM085725.1|BM085725
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|9898733|gb|BE607701.1|BE607701
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|193597269|gb|FK554051.1|FK554051
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|208174645|gb|GD967668.1|GD967668
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGACTTAGAAAAAATGCACTAGCC
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGG-CTT-GAAAAA-TGCACTAGCC
EST: gi|4313567|gb|AI460686.1|AI460686
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|192325659|gb|FK019515.1|FK019515
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTAATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|254328123|gb|GR835088.1|GR835088
EST:     -TGA-GATGAATCA-TTGTTCATCATACTGCTAGTGT-G-TGATGTGGAG                         GGCTTGAAAA-TGCACCTAGCCGCTG
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCAC-TAGCCGCTG
EST: gi|208134410|gb|GD933099.1|GD933099
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAAT
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAAT
EST: gi|10256002|gb|BE823768.1|BE823768
EST:     ATGAAGATGAATCAATTGTTCATCATACTGNNAGTGTTGGTGATGTNNNG                         GGCTTGAAAAATGCACTANNCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|209727250|gb|BW663311.1|BW663311
EST:     CATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: CATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|58018407|gb|CX705149.1|CX705149
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|208198272|gb|GD996413.1|GD996413
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCC
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCC
EST: gi|9258071|gb|BE346218.1|BE346218
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... gcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtcattgggtatgatttgaaatatttgagagctaaaattttgcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG
                                 agctaaa  putative branch site (score: 3)
             tatgatttgaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctaagctgtctagttatggtattgttaaattcagccattctcttagtgtcattgggtatgatttgaaatatttgagagctaaaattttgcacatgtagGGCTTGAAAAATGCACTAGCCGCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC