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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag

Basic information

species Glycine max
transcript GLYMA05G03730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
---GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttg--ttgtcattgaatt-tgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
   || ||||| || ||    ||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| |||||||||||||||||||||| |   | ||| |   |       |||| | |       ||| | |   || | ||   ||        | | || | |||| ||                      
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagta-ctactccttccatctcttctgcggatacctatctgttagtatcttctttgcccactaattaacactaatatcttttcag----------------------

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
---GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca------acttcactctcagtagct-gcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
   || || ||||| ||    |||||  | ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||||| | || |      | | |  |     ||||| | |   | |   | |  | | | |    ||      ||||   |  |  |   |||     | |  ||          
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatcccggcccttactgtacacta---taagtgtgcatgccgctgaaaagaaaaagattatt----------

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g41460.2 (Oryza sativa), 5'ss of exon 2
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca------acttcactctcagtagct-gcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
|| || ||||| ||    |||||  | ||||| ||||| ||||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||||| | || |      | | |  |     ||||| | |   | |   | |  | | | |    ||      ||||   |  |  |   |||     | |  ||          
GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatcccggcccttactgtacacta---taagtgtgcatgccgctgaaaagaaaaagattatt----------

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g21900.1 (Oryza sativa), 5'ss of exon 2
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgt-tgttgtcattgaatttgt-gttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
|| || ||||| ||    ||||| || || || || || | ||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||||| | || |       |  |  |   |  ||||||    | | | ||     |  | | |   |     |||    || ||  |   |  |   | | ||  ||   
GCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagctgtacactataactgtgcacgccgctgaaaagaaaagatta---ttgttggaaattcag--agataatccta---

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatga------ggcaacttcactctcagtagctgcagctgttgttgtcattga-------atttgtgttaacgc---gggtgta---tttatcttttttaagtctttgttggttgattgtacag
|| ||||| |||||    ||||| |||||||| || || ||||| || || |||||||| || ||||||||||| || |||||||| ||||||||||||| |        |  | ||  ||| || || ||||      |   ||| ||||       |||  || |||| |    |||||    |  ||      || ||   |||  |||| ||  |   
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagttaatttgctc-cactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag--

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 2
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagt-ctttgttggttgattgtacag
|| ||||| || || || ||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| |||||||| || |||||||||  |||     ||  | || | ||    |  ||  ||      || |  || |      |  | || |  |||  |    | ||  ||  || |  ||    |   
GCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAAgt--gagtgcgtttttcactaattaagcccccctcctgcgacttttta--ttattactgtgtcgatg-acgtatactagaaacgtatttccttagacgacgacaa--

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: AC203966.5_FGT002 (Zea mays), 5'ss of exon 3
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCAT-GCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
|| ||||| |||||    ||||| |||||||| || || |||||||| || |||||||| || ||||||||||| || |||||||| ||||| ||||||||    |||  || | | | | | ||| || |  |   || |  ||   |   ||    |       ||  ||  |  | |   |       || |  |  | | 
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTTGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATTGCTAAgta---agcatttttagttt-atttgctccaccactaactgcc--tgttctcaagtccttgaaaaaaaataaataatgctgaccccccaaggtgtggcgttgatac

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
 | || ||||| || || || || || ||||| ||||||||||||||||| || || |||||  | ||||||||||||||||| ||||||||||||||||     ||        || |  |  |  || |    |||||| | |   |   ||  |   ||| | || ||  ||  |     ||| |   |  ||||||   
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca--------cttatgatttatagtt----ttgtcaataa---tccattcgcctaggt-tcttgattcttgatctaattttatctatgtattgtag--

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 5'ss of exon 3
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
 | ||||||||||| || || || |||||||| ||||||||||||||||| || || |||||  | ||||||||||||||||| ||||| ||||||||||     |||||         |   ||  |  |  | |  |  ||    ||   ||   ||       |  ||||||| |       || |  |       ||||
TCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAAgtaatcatcaactat-------gggactaaatttcatttctttgttttggtttctttggtgcaaagtcctaaatcttttat-------tggtaatatgaaacacag

upper sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag
 | || |||||||||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||       |  | | ||| | |   |     | | | | | ||  | |||||  ||         | | ||   | |  ||   || | |  |   |  | |||
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagatta-tcttaatcaatatctttat-gatataat--agtttgtaatactttttaaatctctaaaatgtaaaa---ttggcttatgtgtaatgcag

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|209698686|gb|BW656511.1|BW656511
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
EST: gi|23056602|gb|BU577755.1|BU577755
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
EST: gi|18733004|gb|BM527371.1|BM527371
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGT
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGT
EST: gi|209729083|gb|BW655073.1|BW655073
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
EST: gi|192306405|gb|FG997159.1|FG997159
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
EST: gi|8669781|gb|BE190888.1|BE190888
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
EST: gi|6455321|gb|AW186004.1|AW186004
EST:     TCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
EST: gi|120496159|gb|EH224326.1|EH224326
EST:     TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA                         GTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA
genomic: TAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggca ... gattgtacagGTTCTGATGAGCAAAAATTCCTGGAAGCTTCGATGGCTTATGTGTCTGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA