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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgcttaggcaagtcacctccatccagatgtagtgctctacttgttgatagtgaaattttattt...

Basic information

species Glycine max
transcript GLYMA07G00490.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g08300.1 (Oryza sativa), 5'ss of exon 2
GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgcttaggcaagtcacctccatccagatgtagtgct-ctacttgttgatagtgaaattttattt
 || ||||||||||||||||| ||||||||||||||||||| |||||| | |||||||||||||  ||||| ||| ||| | ||||| |||||||||||||||     | |   |   | |||   |   |||   |    |     | |   || |||  |  | |  |    ||   || ||   || |   |  |   
ACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATGAAAGTACATTGGAAGAGAACAAAGTCAGTGAAGTTGGGTTTTTAGTTGTCATGCTTAGTAAGgtaggccgcgtatgtgctgtatataat-ttaaatggtgatgttatttattacgcttcatttaattcttttctgactggatgctgggtgtaacggtgcagca

upper sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G143462_T06 (Zea mays), 5'ss of exon 2
GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgct--taggcaagtcacctccatccag-atgtagtgctcta-cttgttgatagtgaaattttattt
 ||| ||||||||  |||||| ||||| ||||||||||||| |||||| | |||||| ||||||  ||| ||||| ||||| ||||| ||||||||||||||    ||||       | |   |  | | | ||| || |   |||  | |     |   |  || || |     | ||   || | ||  |   | || ||||
ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttctaat----acatctctgtactacacattttcagatagatatgatgttttactgaagtatttttcattttagtctgataatgttaccacttgattt

upper sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgta-tatttctttcttcaagaataccttgccaaacaattgcttaggcaagtcacctccatccagatgtagtgctctacttgt-tgatagtgaaattttattt---
||||||| ||||||||||||| || |||||||||||||||||||   | || |||||||||||  | || || || ||||| || ||||||||||| ||||||  | |||     |   |  |||  ||| ||     | |||     |    |  | |  |||   |  |  |   |||     |   | |||  | ||     
GCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATGAAACTAGCCTGGTGGAGAACAAAGTTACGGAGGAAGGATTTCTCGTCGTTATGCTTAGCAAGgtaacagttcaaatct---ggctac--tgcaaagatcatacttcttttatcttcaacaaatcagtcttcttatttaccttaaacaaggataaaagctgatgaata

upper sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgcttag-gcaagtcacctccatccagatgtagtgctctacttgttgatagtgaaattttattt---
|||||| |||||||||||||| ||||||||||||||||||||||| || || |||||||| ||  | || || ||||||||||| || |||||||| ||||||  | |||   |||     ||   | | | | | | |||||| |  ||||||    | | |  || | |  | || |  ||  ||||   |||  || |   
GCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATGAAACTACCTTGGTGGAGAACAAGGTTACCGAGGAGGGTTTTCTTGTCGTGATGCTTAGCAAGgtacctatctgatttcttt--tatgatcctagatagt-gcttagtgtgagtcactctaagcaacctggatttatata-tccttcttagtcccattagatatagt

upper sequence: GLYMA07G00490.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 5'ss of exon 2
GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgcttaggcaagtcacctccatccagatgtagtgctctacttg--ttgatagtgaaattttattt
 |||||  ||||||| ||||| ||||| |||||||||||||||||| | || |||||||||||  | |||||||||||||| || || |||||||| ||||||  ||| ||| ||      |  ||  |       ||  | |     ||     |    |     ||||  | || |    || ||  | |  | | ||  
ACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATGAAACTACACTGGTGGAGAACAAAGTTACAGAAGATGGTTTTCTAGTGGTCATGCTTAGCAAGgtaggtttttttttttttttctttctatctttgggctttttaacaactgttggtgctgcacttgcatagttgtataataaatttaatgtttaggtatcat--

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|8827362|gb|BE211092.1|BE211092
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298188098|gb|HO032055.1|HO032055
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|213614987|gb|DB957039.1|DB957039
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298164323|gb|HO013968.1|HO013968
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTACGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|213592873|gb|DB969839.1|DB969839
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298167381|gb|HO012644.1|HO012644
EST:     TAGAGAACAAAGTCTCTGAAGACGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|27427422|gb|CA938942.1|CA938942
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|193614977|gb|FK563785.1|FK563785
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|23727295|gb|BU761676.1|BU761676
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|13125598|gb|BG316168.1|BG316168
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298172529|gb|HO019569.1|HO019569
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTGAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|33387852|gb|CA851059.1|CA851059
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|15200810|gb|BI424534.1|BI424534
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|15338030|gb|BI498686.1|BI498686
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
EST: gi|298164600|gb|HO014245.1|HO014245
EST:     TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAG                         AGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG
genomic: TAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttct ... ctatttacagAGTAAAACATCGGGTTCTGCTGCAGCTTCATCTGTTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATGAAACTACATTAGTAGAGAACAAAGTCTCTGAAGATGGTTTTCTTGTTGTTATGCTTAGTAAGgtatatttctttcttcaagaataccttgccaaacaattgcttaggcaagtcacctccatccagatgtagtgctctacttgttgatagtgaaattttattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG