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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgtatgagaggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatatcatatttgacatcactaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 3
-------ttcttgtatgagaggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatatcatatttgacatcactaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA
       ||  |   || |      ||  ||| |       | |  || |  ||  ||||     || |   |   ||  ||| |   | ||||  |     | ||||| ||||| |||||| | || || ||||||||||||||||||||| |||| |||||  |  |  | || |||||||| ||||||||||| || |||||||
gtgttgttttctccctgtggtcgagttt-ttttacatggactta-gtgttcatcagctaaatatgatgtggcaaaagatgtcatt---gcttttggttg--ttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------------ttcttgtatgag---aggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatat-catatttgacatca----ctaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA
                                                                                            |||   |        || ||  |  | |  | |   |   |  | || | |  ||   |   | | |||     ||||      | | |||||||  |     | ||||| ||||| |||||| | || || ||||||||||||||||||||| |||| |||||  |  |  | || |||||||| ||||||||||| || |||||||
gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactacattgaatcccattgattttgcttg--ttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------ttcttgtatgagaggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatatcata-tttgacatcactaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA
                                                    || |  |        |  ||  | | ||  ||  |    ||  | | || |    | || |  ||| || | ||  || | |   |||  |   |   |||||||||   || ||| ||||||| ||||| || |||||||| ||| ||||||||||  |  |||| ||||||||||||||||| ||| |||| |||||||
gtaaaagctttatatgtcctttgaatgatggcaaactgcgttttgcattaacttataattcttagacactttactcttattttagttgttttgaatcttttatttcataaaaaagatagttcgtcaataccactttatttcctatctggacagATTATAGTAAAGATGGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAA

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 4
---ttcttgtatgaga-ggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatatcatatttgacatcactaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA
   | |||| || |   | ||  |  ||    |||   |   |      |  ||||||||   | |  || || |  |  ||| |  |||  |  ||    |||||||||| ||| ||| |||| ||||||||||| |||  ||| ||| ||||||||||||| ||||||||||||||||| ||||| ||||| || |||||||
aaatccttgcatcatccgaatgattcttgatggctgtgttgtaatgcctttatctaatgtt--ttttttaattaatttttctatt--tttataaaaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGTCAAAATGGGTTGCTTTCAACTCCTGCTGTATCAGCTGTCATCCGTGAAA

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|254347113|gb|GR856783.1|GR856783
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|151396774|gb|EV266647.1|EV266647
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|209696727|gb|BW672906.1|BW672906
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|213611739|gb|DB958861.1|DB958861
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|213617812|gb|DB967258.1|DB967258
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|7146923|gb|AW508845.1|AW508845
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|213605046|gb|DB956379.1|DB956379
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|15285957|gb|BI469848.1|BI469848
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
EST: gi|6070595|gb|AW099982.1|AW099982
EST:     CTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAAGGAAGCTATTCCAG                         ATTATAACTAAAATGTCAGCGGCAAATGGAGTAAGACGTGTTTGGATTGG
genomic: CTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAA-GGAAGCTATTC-AGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGG
EST: gi|7684820|gb|AW755468.1|AW755468
EST:     CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAG                         ATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT
genomic: CGCTAGTTGTATCTGGTGATGGTCGTTATTTTTCAAAGGAAGCTATTCAGgtactttttc ... gaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctaatgtcaatatcatatttgacatcactaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA
                                taatgattttaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgtatgagaggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatatcatatttgacatcactaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - tgtatga
- - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - -acatcac