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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacactccgtacttctttctagttcaagattattgctcgaaattacgactttgtccctacgctctcatcggctgaggataagtccaggattttgg...

Basic information

species Glycine max
transcript GLYMA06G11970.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11970.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 5'ss of exon 1
CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgta--tatacactccgt-----acttctttctagttcaagattattgctcgaaattacgactttgtccctacgctctcatcggctgaggataagtccaggattttgg
||| || || || || || || ||||| | ||| ||||||||||||||||| || ||||| ||||| || |||||||  ||||| |||||||||||  |||||  |||| || || |     | ||   || | ||     ||| | |   ||||| | | ||    |  |  ||    || | | |    ||||  ||        
CGCCGGCAAGGCGCCCAAGGGCGACAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCCGCAAGAAGAACACCCTCCGGgtacatatatacgccattaattaattacctcgaatttgctcttaattcatcaaatt-caaattcagacgaattctactctcagttaat--caagtttagacaa----

upper sequence: GLYMA06G11970.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 5'ss of exon 2
CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacactccgtacttctttctagttcaagattattgctcgaaattacgactttgtccctacgctctcatcggctgaggataagtccaggattttgg-----
||| || || || || || || || || | ||| ||||||||||||||||| || ||||| ||||| || |||||||  ||||| ||||||| ||| ||||||   | |  ||  ||        | | ||  | ||    ||   | ||   || ||| | | ||   | || |  | |        ||    | || |     
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCCGCCCGCAAGAAGAACAGCCTCAGGgtaagcaaaaaccacacccaag---attccatcactaa-attcattactaaatctgtgttcat-cgtgattattgattaatttagtcacctaattattcgcccaa

upper sequence: GLYMA06G11970.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G014653_T02 (Zea mays), 5'ss of exon 1
CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacactccgtacttctttctagttcaagattattgctcgaaattacgactttgtcc-ctacgctctcatcggctgaggataagtccaggattttgg----
||| || || || || || || || || | ||| ||||||||||||||||| || ||||| ||||| || ||||| |  ||||| ||||||| ||| ||||||   |||    |  || |      || |  |    |   | |   |    ||  |       |  |    |     ||  |||||      | ||| |     
CGCCGGCAAGGCGCCCAAGGGCGAGAAGACCAACTGGATCATGCACGAGTACCGCCTCGCCGACGTCGACCGCTCGGCGCGCAAGAAGAACAGCCTCAGGgtaagaacaa---gcgctccgccgccgtcc--gtccgtccgttggcgtcgtcaccgtccaaatcaaacaaaaagaacttggcgataatgtgtcgctttcgtaatg

upper sequence: GLYMA06G11970.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G01720.1 (Arabidopsis thaliana), 5'ss of exon 2
CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacactccgtacttctttctagttcaagattattgctcgaaattacgactttgtccctacgctctcatcggctgaggataagtccaggattttgg-----
    || |||||||| || || || |||| ||||||||||||||||||||| |||||||| ||||| || || ||||||||||| ||||| |     |  || |  |   |  | | |    |||  ||||  ||  ||| |  ||  |     | |||  ||         |    |||    | |     |||||| |     
---CGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGA-----ATAGTCT-CAGGgtatggaatcagatctgattcac-atctttgtttcaatctcttgttctgtttctg-------gtaaattgaatcaacggtgttgatttttgcccag

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|58024693|gb|CX711434.1|CX711434
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|298168446|gb|HO009376.1|HO009376
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACA
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACA
EST: gi|58021107|gb|CX707849.1|CX707849
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|21678264|gb|BQ630615.1|BQ630615
EST:     ATCGTCTCGCACACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGCGCTTTGCCGTATGTACAACAAGAAGGGCACGATCGA
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGA
EST: gi|18734175|gb|BM528031.1|BM528031
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|209709358|gb|BW668328.1|BW668328
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|209729783|gb|BW658588.1|BW658588
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|213592504|gb|DB971646.1|DB971646
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|16348414|gb|BI974009.1|BI974009
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|209727657|gb|BW663797.1|BW663797
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|11274975|gb|BF325299.1|BF325299
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
EST: gi|11273926|gb|BF324315.1|BF324315
EST:     ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGG                         TTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG
genomic: ATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacac ... tttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGGGAAAGCTCCTAAAGGGGACAAAAGCAATTGGATCATGCACGAGTATCGTCTCGCAGACGTAGATCGCTCCGTTCGCAAAAAGAACACCCTAAGGgtatatacactccgtacttctttctagttcaagattattgctcgaaattacgactttgtccctacgctctcatcggctgaggataagtccaggattttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC