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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaagccatctagttatggtattgtttaatccagcccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG

Basic information

species Glycine max
transcript GLYMA06G47830.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G800734_T02 (Zea mays), 3'ss of exon 5
--------gctaagccatctagttatggtattgtttaatccagcccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG
           || | ||| |  | |  |||      || |        |  ||    || |    || |  |      ||||   |         | |||||   |||| ||||| || ||  |||    ||| || |||||||||||||||||| | |||||||||   ||||| |||||||| ||||| ||||| |||
tttttttaataaaacaatcaatcttttatatgcccagatgccctttaaatgcttgtactccttttttaaggct----gcatttacaattccgg---taacacaac-agGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCCGAGGGAAGACGGGCTTTACATTTTGCATGTGGCTATGGTGAG

upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
lower sequence: AC215244.3_FGT002 (Zea mays), 3'ss of exon 5
gctaagccatctagttatggtattgtttaatccagc-----ccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG
   |   ||| ||  | |  |     | ||| |||      ||||| ||   | ||  |    | |||| ||      |||    ||||||||  |  || | ||||  | || || |||||||    ||| || ||||||||||||||||| || ||||||||||  || || |||||||| ||||| || || |||
--aacatcatttatctgtcttcacagtaaatacagttgccaccttgcctactgggtt-ttgattttgatatgctgacgttgtcttctaaaattc-atgcaat-agGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG

upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G35450.5 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------gctaagccatctagttatggtattgtttaatccagcccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG
                                  |  |  || ||  |   || ||| || |   |     |||    ||| |  |   ||   | | |   |||| ||    ||    || |  |||| |||| ||||||  |||  | || ||||||| | |||| |||||||||||||| || ||||| || || ||||||||||| |||||||| ||||||
gttagactgcttcctacgttaatatgcttgaccatgtgagatttatcttgcgtgttgcttgaggaattagatgttccaagttttgttttgttgaactcg--ttattggatttttattcgttgattcatt-agGGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAG

upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------gctaagccatc-tagttatggtattgtttaatccagcccttgtctttagtg--tcatcaggtatgatt--tgaaatatttgagagctaaaattttacac-atttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG
                   | ||  |  || |  || ||    | | || |  |  | |       | |   | |||  |  |   |  | || | | || |   | |  |  |  || |   |||| ||||||  |||  | || |||||||   |||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| ||||||
gtaaactgattcatacactgttagtctctcgtgtttctgacggtctatattttatacttaagtcggaatcattgatcgaggttagctcataaactctctgtgcattgatttcctgaaccaaccagGGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAG

upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 3'ss of exon 6
gctaagccatctagttatggtattgtttaatccagcccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacat---ttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG
  ||  | || || | |||  |  ||  |||  |     | |||||   ||       ||  | ||   |   |||| || |   | | ||    |   |||||| ||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||  ||||||| || ||||| ||||| |||
-ttattctat-taataatgacaaagtg-aatatattttgtatctttttagttcgtttttagcaattagcaaggttgaaagtttccactctatttgtaaattagGGTTTGAAGAATGCACTTGCCTCTGGTGCCGACAAAGATGAAGAAGATTCAGAGGGAAGGACTGCACTGCATTTCGCATGTGGGTATGGTGAG

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|6726653|gb|AW311007.1|AW311007
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|151401062|gb|EV270876.1|EV270876
EST:     ATGAAGATGAATCAATTGCTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|254335877|gb|GR847405.1|GR847405
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|254335741|gb|GR847269.1|GR847269
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|17152886|gb|BM142819.1|BM142819
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCCTGACA-GGATGAAGAAGATTC
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGC-TGACAAGGATGAAGAAGATTC
EST: gi|151407493|gb|EV277308.1|EV277308
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTG-TGATGTGGAG                         GGCTTGAAAA-TGCACTAGCCTCTGGTGCTGACAAG-ATGAAGAAGATTC
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTC
EST: gi|192309989|gb|FK002513.1|FK002513
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|254335742|gb|GR847270.1|GR847270
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|21601758|gb|BQ612089.1|BQ612089
EST:     ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA
EST: gi|6726608|gb|AW310962.1|AW310962
EST:     ATGAAGATGAATCNATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAG                         GGCTTGACAAATGCACTAGCTTCTGGTGCTGACAAGGATGAAGAAGATTCA
genomic: ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatata ... acacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG
                                 agctaaa  putative branch site (score: 3)
                                    taaaattttacacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaagccatctagttatggtattgtttaatccagcccttgtctttagtgtcatcaggtatgatttgaaatatttgagagctaaaattttacacatttagGGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - ccatcta
- - - - - - - - - - - - - - - -ccagccc
- - - - - - - - - - - - - - - - - - - - - - - - tgtcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatga