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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA

Basic information

species Glycine max
transcript GLYMA07G36680.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 11
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
||| |   | | ||| | |  ||  | | ||  | ||||   ||||  | | ||    |  |||  ||| ||| | || |||||  ||||||||| || ||||| ||||||||||| || ||||| || |||||||| || |||||||| ||||| ||||| || || ||   |||||||||||| |||
gtatgtgtaat-accatttggataat-gtgtgcttttaa--gcatttatgttctattgccctaagatatctttctcttattgtt-tcagGGTGAGTATTCATGAGGCCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCA

upper sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
||| || |    |  |||||  |   ||   | |  || ||| |||  | |  |  | ||  ||| ||  ||| |  |  |  |  |||||| || || |||||||| |||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||  | ||   ||||||||||||||||
gtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtatt--accaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA

upper sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
|||| |||||  | ||  | |     | | |||||| ||  | ||  |      |||  |          | ||  ||||||| ||||||||||| ||||||||||||||||| || |||||||| || ||||| || || ||||| ||||| |||||||| || || || |||||||||||||| || 
gtaacaaaatgcaactaatga--tagttacttttctgaaggaaatggt----gctgacga----------tataagtttttgtaaccagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT

upper sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 10
gtaagaaaattgacct-tgtaaatccttgagttttc-ttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
||||| ||||  |  |  ||| ||  | |   ||   |   || ||  | | |   | ||  | ||     |  | ||| |    ||  || ||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| ||||| |||||||| |||
gtaaggaaatgtatgtgcgtatattttggtacttcaatcccttgcaaaaatttgtatcat-gtgaacaagaaagtttatatcctctattagAGTGAGCATCCACGAAGCAATGGAACAGCAGAGTATTAGCATATCAAAGGCTGGGATTGTCACTTCTCTCCAGGCTCGCTGCTCTGTCATTGCTGCTGCA

upper sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ17122 (Selaginella moellendorffii), 3'ss of exon 9
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
                               | | ||||   ||    |  | |||    ||| |    |    |||||||     |||||| || || |||||||||||||||||||| ||||| ||||| ||||||||||| || || |||||  | || || || || ||||| || ||||| |||
------------------------------gtattttaaacgcagggcttacattgtc--ttactcggga---gtattttt----tcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA

upper sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
                                        ||  |||    |   | | |  |  |  || |      | | ||  |||||| || || |||||||||||||||||||| ||||| ||||| ||||||||||| || || |||||  | || || || || ||||| || ||||| |||
---------------------------------------gtattttaaacgcagggcttacaatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA

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|15813323|gb|BI785598.1|BI785598
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|27424931|gb|CA936451.1|CA936451
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|208220913|gb|GE018049.1|GE018049
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|207844410|gb|GD814455.1|GD814455
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|193476634|gb|FK439509.1|FK439509
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGGGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|193430045|gb|FK395959.1|FK395959
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCAT
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCAT
EST: gi|193604443|gb|FK555894.1|FK555894
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|207730351|gb|GD708807.1|GD708807
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA
                        cattaat  putative branch site (score: 3)
                                          tttttgtt  putative PPT
         attattatccttgatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC