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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaatatatgcctgatagaagattgccatctctacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA

Basic information

species Glycine max
transcript GLYMA11G31470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 5
tgtgaatatatgcctgatagaagattgccatct-ctacaggtctttgtaatatatatatatataaacagttttatcatttgatg-attgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
  | | | | |||         | |    |  | ||  | |  ||| || |   | |   | |   | ||| |   |||   ||   ||||      | |||||  | ||||| |||||||||||||| ||||||||||| ||||| ||| | ||||| || || || ||||||||||||||||||||  | || || || |
-tttactctctgctcagcttttgctcaataaatactgtaagcatttatattcgctttccct-tgtgctgttctgaaattcattgtgatgttctgtttttcagATTGCTGCTATCTGTCAAGAAGCTGGTATGCATGCTGTGCGCAAAAATCGGTATGTTATCCTCCCCAAGGACTTCGAGAAGGGTTACCGAACCAATGTCA

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
--tg-tgaatatatgcctgatagaagattg--ccatctctacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
  || |   |  ||   | || |   ||||  |   |  |  |    |  ||||  | | | |    |  | |  |  || |   || ||     ||   | |||||  | ||||| |||||||||||||| ||||||||||| ||||| ||  |||||||||| || || |||||||| |||||||| ||  | || |||    
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattat-----gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 5
--tg-tgaatatatgcctgatagaagattgccatctc--tacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
  || |   |  ||   | || |   |||| | |  |  |  |    |  ||||  | | | |    |  | |  |  || |   || ||     ||   | |||||  | ||||| |||||||||||||| ||||||||||| ||||| ||  |||||||||| || || |||||||| |||||||| ||  | || |||||||
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattat-----gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAACGTGA

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 5
tgtgaatatatgcctgatagaagattgccatct-ctacaggtctttgtaatatatatatatat-aaacagttttatcatttgatgattg---ttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
  |  | | |||  | | |  ||||  || | | || |  | | ||| |||   | |   |||  | | |          ||  | | |   |  |    | |||||  | ||||| || ||||| ||||| ||||||||||| ||||| ||  |||||||||| || || |||||||| || ||||| ||  | || |||||||
--ttgaca-atg--taaaatgagatgacctttttctccctggccttgcaattagtttgattattgatctgacacccggaatgccgctcgcattctgcttttacagATTGCTGCTATCTGCCAAGAGGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAAAAGGGCTACCGAACCAACGTGA

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtgaatatatgcctgatagaagattgccatctctacaggtctt-tgtaatatatatatatataaacagttttatcatttgatgat-tgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
| ||| | |||     | |   || |     ||  | || |    ||||||    |||  ||| ||      |||  ||||||  | |||||     |||||||| |||| ||||| || |||||||| |||||||| || || ||||| |||||||| ||||| || ||||| ||||||||||| ||  |  |||| || |
tttgattttatcatgtacatgggaattgttcctaaaaagattgcatgtaatgatgatagttattaatgacactat--tttgattttatgttgaacaatgcagATAGCAGCAATTTGCCAGGAAGCTGGTATGCATGCGGTGCGAAAGAACAGATATGTGATACTACCTAAGGATTTCGAGAAGGGCTACCGCGCAAATGTTA

upper sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 5
----tgtgaatatatgcctgatagaagattgccatctctacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
     | | | | |   |||||||  | |  | |  | |     | |||  |||| |   || | | |   |  |  |  |   |  ||  |    |  |||||||  | |||||||||||||||||||| ||||||||||||||||||||  ||||||| || || || |||||||| |||||||||||| | || || ||||
aaccagcggagaaac-tctgatag--gttcccaaggtttttcattatttcaaataaacgaatttctcatgtgagtgtttttaacacaatc-tgtacgtatgcagATTGCTGCTATTTGTCAAGAAGCTGGGATGCATGCTGTTCGCAAGAACCGATATGTAATTCTCCCCAAGGACTTTGAGAAGGGTTATCGAACCAATGTGA

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|193394727|gb|FK358228.1|FK358228
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAA
EST: gi|254324498|gb|GR833923.1|GR833923
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|193318156|gb|FK286238.1|FK286238
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAG
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAG
EST: gi|207844847|gb|GD813604.1|GD813604
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|208220507|gb|GE017685.1|GE017685
EST:     CTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: CTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|208259049|gb|GE051982.1|GE051982
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|15664967|gb|BI702338.1|BI702338
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|7589710|gb|AW705471.1|AW705471
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
EST: gi|21594594|gb|BQ610203.1|BQ610203
EST:     TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG                         ATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA
genomic: TAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAGgtttgtttct ... gtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA
                              atttgat  putative branch site (score: 5)
     atatatatatataaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaatatatgcctgatagaagattgccatctctacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA

- - - - tatgcct
- - - - - - - - - - - - -tgccatc
- - - - - - - - - - - - - - - - -ctacagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat