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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctacatatctaaaagagatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG

Basic information

species Glycine max
transcript GLYMA17G34690.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g40940.3 (Oryza sativa), 3'ss of exon 5
-tgctacatatctaaaagagatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
 |    |||   ||||  || ||  ||   | ||||   ||  |   ||  |||  ||   |   |  | | |||              |  |||||| ||||||| |||||| |||||||  |||| || || || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| |||||  |||
gtatgtcat-cataaataagttggcatagctctcctgttttgtt---tcacattttatatttacaaaccatgtta--------------taaaaactgcagGCAAGAGGAGACTACCACCGGGATGTCTGTATCATTCCTGTGTCAGCCCATGGTACAAATCCTGCAAGTGCTGCTATGTGTGGAATGAAGATTGTTGCTG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g51410.1 (Oryza sativa), 3'ss of exon 6
tgctacatatc-taaaagagatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
 |  |   ||| ||||  || ||  ||   | ||||   ||  |   ||  |||  ||   |   |  | | |||              |  |||||| ||||||| |||||| |||||||  | || || || || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||  |||
-gtaagtcatcataaataagctggcatagctctcctgttttgtt---tcacattttatatttacaaaccatgtta--------------taaaaactgcagGCAAGAGGAGACTACCACCGGGACGTCTGTATCATTCCTGTGTCAGCCCATGGTACAAATCCTGCAAGTGCTGCTATGTGTGGAATGAAGATCGTTGCTG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g51410.2 (Oryza sativa), 3'ss of exon 5
tgctacatatctaaaagagatgcgatgattttcc-tacattactatctctgattaaattcctgtgatgcttcttacttcttttggccat----tggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
   | | |   ||  | ||      | ||  |   ||   |   ||  ||       ||  |||    | | |||  | |     ||||    |  |||||| ||||||| |||||| |||||||  | || || || || ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||  |||
---tccgtgcttaccacagggtaagtcatcataaataagctggcatagctctcctgttt--tgtttcacattttatatttacaaaccatgttataaaaactgcagGCAAGAGGAGACTACCACCGGGACGTCTGTATCATTCCTGTGTCAGCCCATGGTACAAATCCTGCAAGTGCTGCTATGTGTGGAATGAAGATCGTTGCTG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G104310_T03 (Zea mays), 3'ss of exon 6
tgctacatatctaaaagagatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
      || ||   | || ||  |  |  |  |||   || |      || ||   |||  || ||  || |||     ||  ||   |  ||  || || |||| ||||||||||||||| |||| ||||| || |||||||||||||| || || || ||||| ||||||||||||  ||||||||| |||||  |||
----gtatgtc---atgatatatgtggcctagcct---tttcctctcttggtt---ttctagtaatctttgttaaagaattatgctgataaaa--tgcagTCAAGAGGAGACCACCACCGCGATGTCTGCATCATTCCTGTCTCAGCACACGGCACGAACCCTGCAAGTGCTGCTATGGTTGGAATGAAGATTGTTGCTG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G33010.1 (Arabidopsis thaliana), 3'ss of exon 6
tgctacatatctaaaag-agatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
 |  |||| | | |    | ||  |    || | |||| | || ||||   ||| ||||  | | | |||    | |   |      | || |   |  || |||| ||||| || ||||| ||||| || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| || ||||||||| |  | |
-gtaacatcttttatcctaaatttggatcttattctacctaacaatcttctattcaattg-tattaagctgaaaagtgaatg-aatgaatgcatttttcagTCAAGAGGAGATCATCACCGTAATGTGTGTATCATACCTGTCTCTGCACACGGTACAAACCCTGCAAGTGCTGCTATGTGCGGGATGAAAATTATTACAG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 6
tgctacatatctaaaagagatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
               |   || |    | |||| |   || | || |    |   | | |    |   |  | | |      ||  | |  |   || || |||| || || || ||| | ||||| ||||| |||||||| || ||||| || ||||| |||||||||||||| ||||| ||||||||||||||  | |
-------------gtaagcatacctgtagtttcttgttttccaatatgaactcgcacttcaacaaatttggtaaat-----gggtgaataaatgatgcagTCAAGAGGCGATCATCACAGAAATGTGTGCATCATACCTGTTTCTGCACACGGGACAAACCCTGCTAGTGCTGCCATGTGCGGAATGAAAATTGTTGCCG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------------------tgctacatatctaaaagagatgcgatgattttcctacattactatctctgattaaattcctg---tgatg-cttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
                                                             | |    |   || ||    | |  | ||| |  |   ||  | ||     ||  ||||      ||||| | ||   || | |||    |    |||||| |||| || ||||| || |||||||| || ||||||||||||||||| ||||| || || || ||||| ||||| || ||||||||||||||||||||  |||
gtagactgattcttttcatatttgtaaataattttatcttctgatatgactacttccccatttccctctccttacaatgctttctgttattattattattttttgtcataatttttattctcaacctgatggcatcggtctacctttttgaacaaaaaactgcagGCTAGAGGAGATCATCACCGCAACGTGTGCATTATACCTGTCTCTGCACACGGGACCAACCCTGCCAGTGCAGCAATGTGTGGAATGAAAATTGTTGCTG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 6
tgctacatatctaaaagagatgcgatgattttcctacattactatctctgatt------aaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
     |  | ||  |    |    ||    |  ||  |  ||||  |   | |      ||  |  | |  | ||  |||  |||| |    | || || |||||| |||| ||||||||||||||  |||| ||||| |||||||| || |||||||| || |||||||| |||||||||||||||||||||||||||||  |||
-----ccaaacttcacccaacatcattgcctctctggagcactaatttcaagttgtgtgaagcttgttttttactgattatgtcttctatttaatg-aacctgtagTCAAGAGGAGACCACCACCGTGATGTGTGCATCATACCTGTTTCGGCACATGGGACTAATCCTGCAAGTGCTGCTATGTGTGGAATGAAAATTGTTGCTG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S276_86V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------tgctac-atatctaaaagagatgcgatgattttcc----tacattacta-tctctgattaaattcctgtgatgcttcttacttctt--ttggccattggaa-----actgta----gGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
                                           |||      | | ||     | |  |  ||  ||     || ||| |  | |  ||| |     |  |   | || | |    ||  ||| |   |||||     | ||||    |||  | ||||||   || ||| |||| |||||||| ||||||||||| ||||| ||||| ||||| || || || |||||||||||||| |||||  |||
gtaagacttttgggacattcttctcataagtgctggaagtgtcgctgttgggtttgaatctagttctctctttgcccagcgcactttaatggtgttggatgaggcggcgatcgcgtttttgatggtttgattgacacgtggaatttcgattgtactcagGCTCGAGGAGACGCGCATCGCGATGTGTGCATTATTCCTGTCTCAGCTCATGGAACAAACCCTGCAAGCGCAGCAATGTGTGGAATGAAGATTGTGACTG

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|17519697|gb|BM188739.1|BM188739
EST:     GTGCTGCTGGAGAATATGCCGGACTTATGGTTATTCGTGCATATCATTTG                         GCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACAT
genomic: GTGCTGCTGGAGAATATGCCGGACTTATGGTTATTCGTGCATATCATTTGgtatggatca ... gaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACAT
EST: gi|209728382|gb|BW652039.1|BW652039
EST:     GTGCTGCTGGAGAATATGCCGGACTTATGGTTATTCGTGCATATCATTTG                         GCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACAT
genomic: GTGCTGCTGGAGAATATGCCGGACTTATGGTTATTCGTGCATATCATTTGgtatggatca ... gaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACAT
EST: gi|15589871|gb|BI674487.1|BI674487
EST:     AGAATATGCCGGACTTATGGTTATTCGTGCATATCATTTG                         GCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACAT
genomic: AGAATATGCCGGACTTATGGTTATTCGTGCATATCATTTGgtatggatca ... gaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG
                       ttcttac  putative branch site (score: 2)
     attaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctacatatctaaaagagatgcgatgattttcctacattactatctctgattaaattcctgtgatgcttcttacttcttttggccattggaaactgtagGCAAGGGGAGACCACCACCGCAATGTTTGCATTATACCTGTCTCAGCACATGGTACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT