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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagacttagccaaacacctaaccaaattcgttccatgtgcttttttcaactacttttaactaagctttaggttggtcaattttgcag

Basic information

species Glycine max
transcript GLYMA09G40990.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40990.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os10g35070.1 (Oryza sativa), 5'ss of exon 5
ATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagacttagccaaacacctaaccaaattcgttccatgtgcttttttcaactacttttaactaagctttaggttggtcaattttgcag-----------------------------------------------------------------------------------------------------------
|||| || || || |||   ||||| ||    || ||||| || || || |||||||||||||||||||| || ||||| || ||||| || ||||| ||||| | || |     || | |   || |||  |  |   |  |    ||| ||| ||  ||  | || |   | | ||   ||||   | ||                                                                                                           
ATCTTGTGGCCAACAAAAAGACATTCCCCCACGGGATCAAGGCGCTCGCCGATTATGTTCACAGCAAGGGGCTCAAGCTAGGCATTTACTCCGATGCAGGgta-agagccaagaacataaaaa-aatcaatattttgaaaaataaactttgcaaatagattacaatagg---tggtttaaccaatgcagtagaaatagaagatggagcaaataatctgtggcaaaatatcaatctgtttgttgctccaatctccattttttgttttttttaactgattcttgcgtgcaaatttctgaag

upper sequence: GLYMA09G40990.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G146463_T01 (Zea mays), 5'ss of exon 6
ATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagacttagccaaacacctaacc---aaattcgttccatgtgcttttttcaactacttttaactaagctttaggttggtcaattttgcag-----------------------------------------------------------------------
|  |||| || ||       ||||| || || |||||||| || || |||||||| |||||||||||||| ||||||||||| || || ||    ||||||||| |   ||   ||   | | |  ||   |||   |||||   |  |||||  ||   ||   || |  |  | |  |    ||   |  ||                                                                        
ACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCGCTGGgtacgttctctctccccctctcttctccttcaaacaagttccgatt--tttttgaaatcgctcacaagtgggaatgaattcacccataataccaaagtttccgctacaaggaataggataagtgtatctgttgaactgaaaccggacttctttccttaaattgcag

upper sequence: GLYMA09G40990.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G08380.1 (Arabidopsis thaliana), 5'ss of exon 5
ATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagacttagcc---aaacacctaaccaaattcgttccatg-tgcttttttcaactacttttaactaagctttaggttggtcaattttgcag
 ||||||  |||| || ||||| || ||||||||||| |||||  |||| |||||||||||||| || || ||||||||||| ||||| |||||||| ||||| ||     | ||      | |  |  | | | |  || | || || |||   |||  |     |  |   ||     ||| |    ||| |||
GTCTGGTGCCAAAGAAGTCAACTTTCCCTTCTGGAATTAAAGCGGTTGCGGATTATGTTCACAGTAAAGGCCTTAAGCTTGGGATTTACTCAGATGCCGGgtaaattactattgcttttgcaaattttcctacacttttttcctggtgatttggacaagaatacacatttggcctcatatttgttttggttttcag

upper sequence: GLYMA09G40990.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv10s0071g01100.t01 (Vitis vinifera), 5'ss of exon 5
ATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagactta--gccaaacacctaaccaaattcgttccatgtgcttttttcaactacttttaactaagctttaggttggtcaattttgcag----------
 |||||| || || ||||| ||||| || || || || ||||||||||| || || || |||||||| ||||||||||| ||||| || || ||||| |||||    |||||       ||  ||        ||  |||  |||| |||     |||      || ||  |||| |  |  | | ||  | |           
CTCTGGTTGCTAAGAAATCCACATTCCCATCGGGCATTAAAGCTCTTGCGGACTACGTGCACAGCAAAGGTCTTAAGCTAGGAATCTACTCTGATGCAGGgtaacatgactttctattcaatgcccttttcggtttcttctctgtggtttcc---actttgaaaaattactcttttgtctcat-atttccgtaatgctttgttt

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|193510248|gb|FK467586.1|FK467586
EST:     GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|213595971|gb|DB966274.1|DB966274
EST:     GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|193308916|gb|FK276200.1|FK276200
EST:     GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|208335402|gb|GE135937.1|GE135937
EST:     GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|193335273|gb|FK297985.1|FK297985
EST:     GCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|193391563|gb|FK356462.1|FK356462
EST:     GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTCCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|193529172|gb|FK484363.1|FK484363
EST:     GATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|207805925|gb|GD779158.1|GD779158
EST:     GATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|208132100|gb|GD929011.1|GD929011
EST:     GATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|208066793|gb|GD866480.1|GD866480
EST:     ATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: ATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTA-TTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
EST: gi|213589246|gb|DB957778.1|DB957778
EST:     GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGG                         GTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA
genomic: GATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagac ... aattttgcagGTATTTTACTTGTAGCAAACAGATGCCTGGTTCTCTTGGTCATGAGTTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATGCTGGgtacatagacttagccaaacacctaaccaaattcgttccatgtgcttttttcaactacttttaactaagctttaggttggtcaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG