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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaatgatccactattgtgttagcctgatggatactcctacttttgctctttctctctcaaatatttatggctttgctgtacatttactttaattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTT

Basic information

species Glycine max
transcript GLYMA04G08200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 4
---------------------------cgaatgatccactattgtgttagcctgatggatactcctacttttgc-tctttctctctcaaatatttatggctttgctgtaca----tttactttaattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTT
                           | |    | ||||| |   | ||    ||   | |||  | | || | |   |   | | ||    || |    ||||  ||      ||| |   ||||  |||||  | ||  |  | ||  | |||||||||||||||||||||||||| ||||| |||||||    ||| || || |||||||||||  |    ||||| |
gtatattttctgtagcattctacgatacaagaatttcactaatacatgagatgaattctttctctgattctttcatacattgattttaagctattgtctaattgccatattggttttttcaccaattttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGTGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCAT

upper sequence: GLYMA04G08200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------------cgaatgatccactattgtgttagcctgatggatactcctacttttgctctttctctctcaaatatttatggctttgctgta--catttactttaattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTT
                                                                                      | || |  | | | |   | |  |    ||||| |    ||  | | ||  | | |    |    |||| |||  | |   |||||  |||| ||  |||||  | ||  |  | ||  | |||||||||||||||||||||||||| || || |||||||    ||| || || |||||||||||  |    ||||| |
gtatattttctatagcattctgcgatccaataactccatgactacatgagatgaaattctttctctgatacacgattttttaagttattgttttattgtcgcaatggtttctctgatacacgattttaagttgttgttttattg--tcgcaatggttttttttttaccattttttttatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCAT

upper sequence: GLYMA04G08200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g02850.t01 (Vitis vinifera), 3'ss of exon 4
cgaatgatcc--actattgtgttagcctgatggatactcctacttttgctctttctctctcaaatatttatggctttgctgtacatttactttaattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTT
   ||| ||   |   |||  ||    |  |  |          || ||||| ||  |      ||    ||  |||  ||    ||| ||    |||||||||  |  ||||||| || ||||| ||||||||||||||||| |||||||||||  |||| |||| | | ||||| || ||||||||  || | || ||||
-atatgctcaggatatttgaatttagattgtaaagggataagaattggctctatcattgatgtttacacttgattttattg-gtgttttctgggcttggcagAACATGCTAGAGACTGGCTTAATAGTTGGTGGATGGGATAAGTATGAAGGTGGTAAAATATATGCAATCCCTCTTGGAGGAACAATTATAGAGCAGCCTT

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|10709899|gb|BF009623.1|BF009623
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|58022364|gb|CX709105.1|CX709105
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|58022573|gb|CX709314.1|CX709314
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|19934684|gb|BQ079714.1|BQ079714
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|58016325|gb|CX703067.1|CX703067
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|298174239|gb|HO017575.1|HO017575
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|23730341|gb|BU763264.1|BU763264
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|254320192|gb|GR829380.1|GR829380
EST:     CAGTTAAAGTTGCTGC-AACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|254320191|gb|GR829379.1|GR829379
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|13311784|gb|BG405435.1|BG405435
EST:     CTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|213619813|gb|DB969477.1|DB969477
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|33388670|gb|CA851877.1|CA851877
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|298192887|gb|HO033321.1|HO033321
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAGATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|15813603|gb|BI785878.1|BI785878
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
EST: gi|58019397|gb|CX706139.1|CX706139
EST:     CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG                         AATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT
genomic: CAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAGgtttgacctt ... taattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctttctctctcaaatatttatggctttgctgtacatttactttaattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTT
                                          ctttaat  putative branch site (score: 4)
                                      tttacttt  CT-rich tract
                                  tacatttactttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgaatgatccactattgtgttagcctgatggatactcctacttttgctctttctctctcaaatatttatggctttgctgtacatttactttaattggcagAATTTCTTAGAGACCGGGTTAATTGTTGGTGGATGGGATAAATATGAAGGTGGACAAATTTATGGAGTTCCTCTGGGTGGAACAATAGTACAACAACCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - -agcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgta