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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggatccagttgttgatgtctttggattagggtttggttcctttgtttcgatctgtttcggatcatgttctgt...

Basic information

species Glycine max
transcript GLYMA07G01440.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 1
--GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggat-ccagttgttgatgtctttggattagggtttggttcctttgtttcgatctgtttcggatcatgttctgt
  |  |  | || ||| ||  | || |  |  |||||||||| |||||||   ||| ||||||| |||||||||||  ||||||||||||| || ||||||||| |     |  || ||      |  || | | |  |  |     |||    |  | | |     | |||  ||   |  | |  |  |     |||  | 
GCGGAGGCGGCGAGGCGGCCGCAGCCG--CAGCCGCAGCCGCGGGAGTGGCGGTTCGCGCAGGTCTTCGGGGAACGCGCGGCGGGGGAGGACGTGCAGGAAGgtgagaac-gcgccgacccgcccccttccgctgctcgccgcgtgcgtcgcgtggctcgtgagatctgcctcggtccggggcgggatgtgggagggtttcga

upper sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggatccagttgttgatgtctttggattagggtttggttc--ctttgtttcgatctgtttcggatcatgttctgt---
|||||   ||  ||  |  | |||  ||| |||| ||  ||||||||||||||||| ||||| ||||| || ||  |||| || |||||||| |||||||||| ||||||    |   |||    || ||||||     ||| || | |    |||||||||||||   | | |||| |||||||||| |      ||  ||   
GATGACACCGCAGCTCCCTCCGCGCCTCCTCCGCCGCAACTGGAGTGGAAATTCTCTCAGGTATTCGGCGAGCGGGCGGCCGGCGAGGAAGTGCAGGAAGgta-ttgttggcttt---ttgcggcgttggatccgccaattgttg-cgtgaatttagggtttggttttgcgtagttttgatctgtttctggatcgattaggtttt

upper sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggatccagttgttgatgtctt-tggattagggtttggttcctttgtttcgatctgtttcggatcatgttctgt--
|  |     |  ||  || |  | |  |||  ||   |||||||||||||||| || |||||||||||||| ||| |    ||||| ||||| || |||||||  |||| |   | ||  |||  || ||    |   ||   | ||   ||   ||| |   |||    | | ||   ||  ||     |||  |   |   
GGGGCCCCGGATGCCACTTCTTCTGCGCCATTGCCTGCGCTGGAGTGGAAATTTTCTCAGGTTTTCGGGGAGCGTGCCATCGGGGAAGAAGTGCAAGAAGgta--tgttatggat-cgcagttgcgttggggggaagagtgtgtatcccgtgaggtagtgcggggtggtgtggattatttcccttgtttttcagttctcgaga

upper sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggatccagttgttgatgtctttggattagggtttg--gttcctttgtttcg--atctgtttcggatcatgttctgt--
   |    || |    |   |      ||   ||  ||||| ||||||||||||||||| || ||||| |||||| | |||||||| |||||||| ||||||       | ||  |  || |  | |  | | || |  | |  |   ||| || |    | |  |||  | ||  |||    ||||| |  ||    |||     
CCCGCTCCCGGGTTGCCAATGAGCCAGCCTTTGCCTCCGCTTGAGTGGAAATTCTCGCAAGTGTTCGGAGAACGTGCTGCGGGGGAAGAAGTTCAAGAAGgtg-----cggtcacattttatgttttttgtttcactgatcggagctcttg-atcatccatcgctgttgttgtgactcgtggactgttgcttattgcattccactt

upper sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 1
GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggatccagttgttgatgtctttggattagggtt-tggttcctttgtttcgatctgtttcggatcatgttctgt-----
      |     |   ||   || |  |||  ||   || |||||||||||||||||||||||||||| || ||| |    || |||||||| || |||||||     || | ||   | ||  | | |     ||||   |||||     ||  | | |  || || |   |  |   |  |    ||    ||   |||     
CCCACTGCTACTGGTTCTGTTGCTGCGCCATTGCCCGCGTTGGAGTGGAAATTCTCGCAGGTTTTCGGCGAGCGTGCCATCGGAGAGGAAGTGCAAGAAGgta-----tggttctggatcgtcgtat-gttggtagtttaggatgttcggagaagaagatcgtgttttccgcgagttagtgggggctggtgtctggattgtttcct

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|33389971|gb|CA853178.1|CA853178
EST:     ATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: ATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttg ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|207824963|gb|GD797179.1|GD797179
EST:     CGGCCGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
genomic: CGGCGGGGGAGGAAGTTCAGGAAGgtaattgttg ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA
EST: gi|208259705|gb|GE059735.1|GE059735
EST:     CGGGGGAGGAAGTTCAGGAAG                         TGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGGTCATCTTGCTA
genomic: CGGGGGAGGAAGTTCAGGAAGgtaattgttg ... atttcttcagTGGATATAATTTCTGCTATTGAATTTGACAAGTCTGGTGATCATCTTGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGAGGTCGTGGCAGCTCCGGCGGGTCCACCGCAGCCGCTGGAGTGGAAATTCTCGCAGGTTTTCGGGGAACGTACGGCGGGGGAGGAAGTTCAGGAAGgtaattgttgttcctacgttgttctgtcggatccagttgttgatgtctttggattagggtttggttcctttgtttcgatctgtttcggatcatgttctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA