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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacatgccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG

Basic information

species Glycine max
transcript GLYMA11G37770.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacatgccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                               |||| |||   | |   |      | |||   ||  ||  | | ||  |  | |  ||  |     | |||     ||| ||      ||    | | |||||||||||||||||||||| ||||| |||||||| |||||  |||| |||   ||||| ||  |||| |  |||
----------------------------------------------gttaacatacaaatacaacttattcacaaacgcgtataattttacaaaacgttttcgaaactaagaagaaac-----actttttaatgattcaataaacagCCTGCACATGAGAAGATTGGTGTTGTGGATTCTCAATGGATCATTCATCAAAAGATTCCTTCTTTAGGCAGCCAG

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 11
gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacat-gccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                                   | ||| ||  | ||| |   |     |   | ||| | |         | | |   |   | | ||    ||||   ||  |   |     | | ||||||||||||||||||| |||||||| |||||||| |||||  | || |||  | |||| ||  |||| |  |||
---------------------------------------------------gttaatcattttgcctacataccttgactcttaaatacactggacatgtgtttggtaagttatcta---ctaaaaagtttcctaataaaacaaacagCCTGCACATGAGAAGATAGGAGTTGTGGATTCTCAATGGATCATACATCAATCTCTTCCTTCTTTAGGCAGCCAG

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 12
gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacatgccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                 |     | |  || | ||| |       || ||   |||| | | |||    ||| |   |    ||||| | ||   |   ||  | ||  |||| | |        ||  ||||||||||||||||||| ||||| ||||||||||| ||| | ||||| |||  | |||| || || || || || 
------------------------------gtaagaaaagagacacttgaagttcgttgtttgtcacgcaaaagacagagtttctaatta---tatcgtctgttatatgacg---aatctgaatatattttacaccga--aatgcagCCTGCACATGAGAAGATAGGAGTAGTTGATTCTCAATGGGTCGTTCATCAATCTTTTCCTTCCCTTGGCAACCAA

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacatgccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                                    |    |  ||| |  ||   |     | |        |  ||    |   || ||| |    | |  ||  |   | ||| | |||  || | ||||||| |||||||| ||||||||||| |||||||| |||||  |||| |||  | ||||||| || ||||| |||
--------------------------------------------------gtactgacctatgtc--tgcctacttctaattctcttatatcatttgtttgttagcatgcatgatcatattggaacttcctcgtcttt--gaaacagCCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCATTCATCAAACTTTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacatgccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                                    |    |  ||| |  ||   |     | |        |  ||    |   || ||| |    | |  ||  |   | ||| | |||  || | ||||||| |||||||| ||||||||||| ||||||||  |||| ||||| |||  | ||||||| || ||||| |||
--------------------------------------------------gtactgacctatgtc--tgcctacttctaattctcttatattatttgtttgttagcatgcatgatcatattggaacttgctcgtcttt--gaaacagCCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAAGGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S70_58V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------gtgagtccatt-ctcacatt-ttctcaaatcgtct----aatttggtgtgaccttaagataagcacatgccaat----gaaaaaaaaaagtgaaaaataaaaatgcaatctgtaac--attctgtgtaactttaaactatt------ctcctttttctgatat--agCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG-------------------------
                                ||  || ||   || ||||   | || ||| |  |    || | |     | |||  |   |   | | | | |    |||  |  |   ||     ||      || ||| |  |  | |   || |  | | | ||| |       |  | ||  |||| |  ||||||||||||| || ||||||||||| ||| ||||||||||    || |  | | | |  || |||   |    |                         
gtaagtttatacgaagttgaatttcgtcagtcgtaggtgcagagcttacataactttctaattgcatcaacaaatggacacaagcttcggtggacttctttctactagttgaagtatcactctggttgttattttctcagtctctgtctgaattgttggatatctcatctactgaatggtttgtcttgatgatttgcagCCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCGGTTTGTGTTCCTCACAACCATTCAC

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S70_58V6.2 (Physcomitrella patens), 3'ss of exon 12
--------------------------------gtgagtccatt-ctcacatt-ttctcaaatcgtct----aatttggtgtgaccttaagataagcacatgccaat----gaaaaaaaaaagtgaaaaataaaaatgcaatctgtaac--attctgtgtaactttaaactatt------ctcctttttctgatat--agCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                ||  || ||   || ||||   | || ||| |  |    || | |     | |||  |   |   | | | | |    |||  |  |   ||     ||      || ||| |  |  | |   || |  | | | ||| |       |  | ||  |||| |  ||||||||||||| || ||||||||||| ||| ||||||||||    || |  | | | |  || |||   |    |
gtaagtttatacgaagttgaatttcgtcagtcgtaggtgcagagcttacataactttctaattgcatcaacaaatggacacaagcttcggtggacttctttctactagttgaagtatcactctggttgttattttctcagtctctgtctgaattgttggatatctcatctactgaatggtttgtcttgatgatttgcagCCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCG

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|58024808|gb|CX711549.1|CX711549
EST:     ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtccat ... tctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|51337681|gb|CO981547.1|CO981547
EST:     ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtccat ... tctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|57574426|gb|CX547401.1|CX547401
EST:     ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtccat ... tctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|16996411|gb|BM085783.1|BM085783
EST:     ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtccat ... tctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|192315451|gb|FK009225.1|FK009225
EST:     GCTTGGTCCATGGGTGGGGTCTTGATTTTGTTCTTAGAAAATGTGTTGAG                         CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtccat ... tctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
EST: gi|57574192|gb|CX547167.1|CX547167
EST:     ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA
genomic: ACTTGGTCCATGGGTGGGGTCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtccat ... tctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG
                                            ttctgat  putative branch site (score: 3)
                                ctattctcctttttct  CT-rich tract
                      taactttaaactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtccattctcacattttctcaaatcgtctaatttggtgtgaccttaagataagcacatgccaatgaaaaaaaaaagtgaaaaataaaaatgcaatctgtaacattctgtgtaactttaaactattctcctttttctgatatagCCTGCACATGAGAAGATTGGAGTTGTTGATTCTCAGTGGATTGTTCACCAAGGTATTCCCTCACTAGGGAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA