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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTCTTTTGTATATTGTACCTTCTGTAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttcattgcttagttttctgatttctttgttctcatatcaatgttaatcatcctttttatgcatctagtttgctttcaatcattagttttactt...

Basic information

species Glycine max
transcript GLYMA04G08510.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 11
CCTGCTCTTTTGTATATTGTACCTTCTGTAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttcattgcttagttttctgatttctttgttctcatatcaatgttaatca---tcctttttatgcat--ctagtttgctttcaatcattagttttactt
||||| ||| | |||||||||||  | || ||||||||| |||||||||||||| |||||||||| || || |||| |||||||||  ||  |||    || |  ||| ||| | ||  |   ||||||| ||    ||| ||||||  ||  |||  || || ||  || || |||      
CCTGCACTTCTTTATATTGTACCAGCAGTTATTGGATTTATGGCTGCTCATTGCATATGGAATGGCGAAGTTAAACCGgtttgtttg-ataactttaccttat--tttgtttctcctatttataatgttattcgcattccattttatatataactacatttctgtctttctttggttggtt--
















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|193659073|gb|FK603388.1|FK603388
EST:     TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAG                         TTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
genomic: TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttc ... atcaacgcagTTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
EST: gi|6915891|gb|AW397421.1|AW397421
EST:     TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAG                         TTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
genomic: TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttc ... atcaacgcagTTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
EST: gi|193623129|gb|FK577727.1|FK577727
EST:     TATGGAATGGTGATGTCAAACAG                         TTGTTGGAGTTCGGTGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
genomic: TATGGAATGGTGATGTCAAACAGgtttgttttc ... atcaacgcagTTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
EST: gi|120494250|gb|EH222417.1|EH222417
EST:     TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAG                         TTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
genomic: TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttc ... atcaacgcagTTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
EST: gi|192327708|gb|FK020699.1|FK020699
EST:     TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAG                         TTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
genomic: TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttc ... atcaacgcagTTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
EST: gi|14011195|gb|BG726048.1|BG726048
EST:     TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAG                         TTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT
genomic: TAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttc ... atcaacgcagTTGTTGGAGTTCGATGAGTCAAAGACTGCCAATTCACCTCAAGAGAGTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTCTTTTGTATATTGTACCTTCTGTAATTGGATTTTTGGCTGCTCATTGCTTATGGAATGGTGATGTCAAACAGgtttgttttcattgcttagttttctgatttctttgttctcatatcaatgttaatcatcctttttatgcatctagtttgctttcaatcattagttttactt

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