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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttaatgtattatagtgctatactttatcttgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC

Basic information

species Glycine max
transcript GLYMA17G01360.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
----gtgcttaatgtattatagtgctatactttatcttgccctgtaatgc-aatttgactaagcctc--aatgttggtatatatttccattt--agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC-
        |||  ||  |    |     || | |  ||   ||| |  |    |   |||||| | |  | || || |  | ||||   |||  ||||||| || || |||||||||||||||||||||   |||||||| ||||| ||||||||||||||     ||||    ||    | |  ||||  | ||| 
gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCG-CACATTTCAGAGGCC

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 3
-------------------------gtgcttaatgtattatagtgctatactttatcttgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC
                          | |||  | | || ||     || |||| |  ||    |  || | | |    ||  | |      | || |   | |   |||||||||| || || ||||| |||||||||||||||   ||||| ||||||||  |||||||||||||     ||||   |||    |     || || || |
gtaaagactgggaatattgtttaactttcttggtctcttctaacaggattctttctgctgaaagg--ataccagtaacttagacatgctcactagtct---tgttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
----gtgcttaatgtattatagtgctatactttatcttgccctgtaatgcaatttgactaagcc--------tcaatgttggta----tatatttccattt----agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC
     || | |  ||  | |       ||||  || |  | |   |||||| || |  | | |         ||| | ||  ||     || |   ||| |    ||||||| ||||| || || ||||| |||||||||||||||||||||||||| |||||||| |||||||||   ||  |||| || ||   ||| | ||| |
gtaattgatcatggtcctgtctcctcgtactaaatttc-caccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------------gtgcttaatgtattatagtgctata-ctttatcttgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccattt-agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC
                        |     ||   |||| |  |||| | | | |      |  | | || ||      | |   | ||  ||  |||  |||| |  || ||||||| || ||||| |||||||||||| | ||||||||||||||||| ||| | ||||| |  |||  | ||||  ||||| || |||  || | |||| 
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
gtgcttaa--tgtattatagtgc-----tatactttatcttgccctgtaatgcaatttgactaagcctcaa--tgttggta-tatatttccat---ttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC
||| |||   | |||  ||||       | || || | |||  | |||  || ||||    ||   ||     | ||| || | | |||  ||   ||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| |||    ||||| |||| |||  |  |  |       
gtgtttatcttatatgctagtatatgtgtgtatttgaactttacttgtt-tgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA

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|13181599|gb|BG352939.1|BG352939
EST:     CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAC                         GTTGCCAAGATAGAAAC
genomic: CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAAC
EST: gi|208279339|gb|GE080826.1|GE080826
EST:     CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|19348946|gb|BM893478.1|BM893478
EST:     CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|208311116|gb|GE108520.1|GE108520
EST:     CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: CAATGCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|5342423|gb|AI794707.1|AI794707
EST:     GAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: GAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|207710299|gb|GD689765.1|GD689765
EST:     AACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: AACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC
               atttgac  putative branch site (score: 4)
                                            tttccattt  putative PPT
                                      tatatatttccattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttaatgtattatagtgctatactttatcttgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA