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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacatgcatagatgcatgaagacttataatggcttaatcattttattgtgtttcttttctttatttgtgtaattttgtaacttctgttttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCAT

Basic information

species Glycine max
transcript GLYMA15G17330.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G17330.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143767_T01 (Zea mays), 3'ss of exon 3
catacatgcatagatgcatgaagacttataatggcttaatcattttattgtgtttcttttctttatttgtgtaattttgtaacttctgttttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCAT
                          ||  ||  | |||  | ||  || |  |   |||          |   |||  || | | |  |||    |||| || || ||||||||    |||||||||||||||||||| |||||||| |||||||| || || |||||| | || ||||||||||| || || || || 
-------------------------gta-gatatcataa--acttgcttatactctgttttacggcaccggatgtttactatcgtttaatttg--ctcagTTTCGACAAGATCATTGCGAAGGAAATCCCTTCGAGCATCGTATATGAAGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCAC

upper sequence: GLYMA15G17330.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g01610.t01 (Vitis vinifera), 3'ss of exon 3
catacatgcatagatgcatgaagacttataat--ggcttaatcattttattgt-gtttcttttctttatttgtgtaattttgtaacttctgttttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCAT
  | | |          |  || ||| |||||   |    |  | |||  |   |      ||||| |||   |  || |  ||   | || | |  |||||||||||| ||||| |||  |||||| || ||||| | |||||| |||||||||||||| ||||| |||||||| ||  | || ||||| ||||| ||||||
--ttcgtaggactccatagtaatactaataattcagtcagacaagttttctacagagaaagttcttgattgcagccatatgatagaat-tgatgttttttcagATTTGACAAGATTATAGCTAAGGAGATTCCTTCAACCATTGTGTATGAGGATGAAAAAGTTCTAGCATTTCGGGATGTCAACCCACAAGCTCCAGTTCAT
















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|192303106|gb|FG994224.1|FG994224
EST:     GCTACAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|16342657|gb|BI968252.1|BI968252
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|16283453|gb|BI945558.1|BI945558
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|16349218|gb|BI974813.1|BI974813
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|298184576|gb|HO029789.1|HO029789
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATGAGGAAATCCCTTCGAGCATTGTATATGGGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|6482492|gb|AW201749.1|AW201749
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|31560970|gb|CD486808.1|CD486808
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|18692831|gb|BM521679.1|BM521679
EST:     GCTACAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
EST: gi|298168753|gb|HO009683.1|HO009683
EST:     GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAAT                         ATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA
genomic: GCTGCAGCAAAAACAGCAGCTGTTAATTTTGATAGTGAAGCTCCAACAATgtagcagccc ... ttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtgtttcttttctttatttgtgtaattttgtaacttctgttttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCAT
                               ttgtaac  putative branch site (score: 2)
                                     cttctgttttcatttc  CT-rich tract
           ttttctttatttgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacatgcatagatgcatgaagacttataatggcttaatcattttattgtgtttcttttctttatttgtgtaattttgtaacttctgttttcatttcagATTTGATAAGATCATAAATAAGGAAATCCCTTCGAGCATTGTATATGAGGATGAAAAGGTTCTTGCATTTCGTGACATTAATCCACAGGCTCCGGTTCAT

- -acatgca
- - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttctg