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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacttcaccaaatgcttttaattattgctttctcctttattcaattttatgggcttttctatctatcaggggcaataatattctgatcaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGACAACCTAGGTTCCGCAGCATGTGGGAACGTTACT

Basic information

species Glycine max
transcript GLYMA01G40210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G40210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 2
gtaagt-tcacttcaccaaatgcttttaattattgctttctcctttattcaattttatgggcttttctatctatcaggggcaataatattctgatcaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGACAACCTAGGTTCCGCAGCATGTGGGAACGTTACT
|||||| ||| ||    || |   |||| | | |   |      | ||    | | ||||       | |  ||| |  |  |  |   | |  | |    ||  ||  ||  |     || |||||||| ||||| || ||||| ||||| ||||| |||||||| || |||||||||||||| |                                 
gtaagtatcagtttcttaatta--tttattcacttgctgaattataatgatttctcatggatcaccatgta-atctgcagACAGGAGGCTTTAGTGAGGACATGATT-CCTACT-----GTAGGATTCAACATGAGAAAGGTGACCAAAGGTAATGTCACAATAAAATTGTGGGATCTTGGAGGCC---------------------------------

upper sequence: GLYMA01G40210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
gtaagt-tcacttcaccaaatgcttttaattat-tgctttctcctttattcaattttatgggcttttctatctatcaggggcaataatattctgatcaatttattgtt-atctgattccag-
|||||| | |      |   || |   | | || | ||   |  || ||  ||| |  |   | ||  ||   | || |     |   |  |||     |||| ||   || |||| ||    || |||||||||||||| ||||| || ||||| ||||| || |||||||| |||||||||||||| |                                 
gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggta---aacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------

upper sequence: GLYMA01G40210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007188_T01 (Zea mays), 3'ss of exon 2
gtaagttcacttcaccaaatgctt-ttaattattgctttctcctttattcaattttatgggcttttctatctatcaggggcaataatattctgatcaatttattgtt-atctgattccag-
||||||     |||     | |||   |   ||    |     | || | || | ||||     ||| ||  |   |      |   |  |||     |||| ||   || |||| ||    || |||||||||||||| || || || ||||||||||| || ||||| || |||||| ||||||| |                                 
gtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattc-ataaacatgtattttttgcagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAGGTTACCAAAGGGAATGTGACGATAAAATTGTGGGATATTGGAGGCC---------------------------------

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|209719919|gb|BW666002.1|BW666002
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAACCGCTACAATAAAGTT
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAAT-GTTACAATAAAGTT
EST: gi|192309196|gb|FG999437.1|FG999437
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|209713657|gb|BW679369.1|BW679369
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|21600628|gb|BQ610959.1|BQ610959
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|193614466|gb|FK563218.1|FK563218
EST:     CTACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGTCAAAAGGGAATGTTACAATAAAGTTA
genomic: CTACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192326131|gb|FK016958.1|FK016958
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|298198680|gb|HO042043.1|HO042043
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151402581|gb|EV272394.1|EV272394
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|298181019|gb|HO022458.1|HO022458
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192299066|gb|FG990394.1|FG990394
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151411975|gb|EV281786.1|EV281786
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|213608988|gb|DB962914.1|DB962914
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192315185|gb|FK010009.1|FK010009
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|37996453|gb|CF808042.1|CF808042
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192325013|gb|FK015434.1|FK015434
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|209712282|gb|BW668476.1|BW668476
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|15813605|gb|BI785880.1|BI785880
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|213597753|gb|DB960310.1|DB960310
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|209715505|gb|BW682171.1|BW682171
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58014594|gb|CX701336.1|CX701336
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58018793|gb|CX705535.1|CX705535
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192309197|gb|FG999438.1|FG999438
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192315186|gb|FK010010.1|FK010010
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|8827780|gb|BE211510.1|BE211510
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|213614589|gb|DB969138.1|DB969138
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|298183805|gb|HO029018.1|HO029018
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACTGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatctatcaggggcaataatattctgatcaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGACAACCTAGGTTCCGCAGCATGTGGGAACGTTACT
                 aataatattctgatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacttcaccaaatgcttttaattattgctttctcctttattcaattttatgggcttttctatctatcaggggcaataatattctgatcaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGACAACCTAGGTTCCGCAGCATGTGGGAACGTTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA