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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgctgatgtggaaataaagagaacttatgatttgcatagtttaactttccttggttgattcttttgctcaagaagtttaaatatttctgttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGATGGTCTTTGGAAG

Basic information

species Glycine max
transcript GLYMA04G41130.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41130.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S215_25V6.1 (Physcomitrella patens), 3'ss of exon 6
----------aatgctgatgtggaaataaagagaacttatgatttgcata-----gtttaacttt-----ccttggttgattcttt-----tgctcaagaagtttaaatatttc----tgttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGATGGTCTTTGGAAG
            |||||||   |    ||       || |  ||     |     ||||||| ||       || ||| |||         ||  ||  |  ||| | | ||||       |||| ||| ||    ||||| ||||||||||| || |||||| |||||||||||||||| || || ||||||
gtacgttatgtttgctgatcccgtttcaattttgttttctccttgatgaactagtgtttaacattaaacttgttcgttaattacccgggactgagcactagatttgactgtttcgccgcaatgttacagTAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG
















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|193363966|gb|FK333048.1|FK333048
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|151410220|gb|EV280035.1|EV280035
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|58016274|gb|CX703016.1|CX703016
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|193566211|gb|FK524616.1|FK524616
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATCATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|208047854|gb|GD845245.1|GD845245
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|151395221|gb|EV265092.1|EV265092
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|298176588|gb|HO023175.1|HO023175
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTT
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTT
EST: gi|193364720|gb|FK330135.1|FK330135
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|298176132|gb|HO015537.1|HO015537
EST:     AAACAGCATGCTCTCGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCGATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|208333078|gb|GE127383.1|GE127383
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|193691396|gb|FK633643.1|FK633643
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGCCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|10847978|gb|BF070551.1|BF070551
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         TAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|298173235|gb|HO020219.1|HO020219
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCT
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCT
EST: gi|208134219|gb|GD931354.1|GD931354
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|193414426|gb|FK379218.1|FK379218
EST:     GGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: GGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
EST: gi|151413172|gb|EV282980.1|EV282980
EST:     AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACAT                         AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA
genomic: AAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCAGCAAAAGACATgtaagaaact ... gttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttccttggttgattcttttgctcaagaagtttaaatatttctgttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGATGGTCTTTGGAAG
                                        tttctgtt  CT-rich tract
                          aagaagtttaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgctgatgtggaaataaagagaacttatgatttgcatagtttaactttccttggttgattcttttgctcaagaagtttaaatatttctgttgtttcagAAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGATGGTCTTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- tgctgat
- - - - - - -aaataaa
- - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - ttccttg