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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagttttgtcttttgtgttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt...

Basic information

species Glycine max
transcript GLYMA06G18150.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagttttgtcttttgt-gttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt--
||||||| ||||||||||| || || |||||||||||||||||||| |||||||| |||||||| || || || ||||||||||| ||  |||| || ||||  | ||||  | | |     ||  |||   | ||  | || | ||    | | ||| |||   |    |  |   |    |   | || | ||||  |   
TCTGCGTGTACTGCCCCGGAGGCCCCGACTCCGACTTCGAGTACAGCACCCAGTCCTACACCGGCTACGAGCCCACCAGCATGCGCGCCATTCGAGCAAGgt--gatttacctcactggctactgatgtcacttggaaatactataccacctgtgaga-tgagctgcacggcgatgctttctctagtgttgttttgaagtatg

upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgtta-gttttgtcttttgtgttagggtaaacgaaactgtttttaagag---tgaatagttgagtcaaattaatccctatattctgttgatttt
|||| ||||||||||| || || || |||||||||||||||||||| || || || ||||| || || ||||| ||||||||||||||  |||| || |||||   |   ||    |  |||   |   || |    | |||     |  ||| ||      || |     ||||  | | | | | | | || ||||      
TCTGTGTCTACTGCCCGGGCGGTCCCGACTCCGACTTCGAGTACAGCACGCAATCCTACACTGGATACGAACCCACCAGCATGCGTGCCATTCGGGCAAGgtaatttcactggagtgcattggtgtccatgcttcctttaactgcttttatttaaacttttctgtacctaggagtgcagtgacttcgtgt-ttgtgttaca---

upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G359735_T03 (Zea mays), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagtt-ttgtcttttgtgttagggtaaacgaaac-tgt---ttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt
|||| |||||||||||||| || || || ||||||||||||||||| || || || ||||| || || || || ||||||||||||||  |||| || ||||  | ||||  | | |   |||   |   | |     | || | || |||   || |   | ||  |   |   | ||  || |  |  | ||  | | |    
TCTGTGTCTACTGCCCCGGCGGTCCCGATTCCGACTTCGAGTACAGCACGCAATCCTACACGGGATACGAGCCCACCAGCATGCGTGCCATTCGGGCAAGgt--gatttagctcactggctgttgatgccgctgataaatactacacatgtaccttcttgtattgcttgaattgatgaaggtagtatccttgtttaggttag---

upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagttttgtcttttgtgttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattct-gttgatttt-----------
| ||||| || || ||||| ||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| || ||||||||||| ||  |||| || ||||   |        ||   |||||| ||||||| || ||  ||||||  | |||    |      ||||   |    |     |    | | | |  ||||           
TATGCGTTTATTGTCCCGGTGGACCTGACTCTGACTTTGAGTATAGTACTCAGTCTTACACTGGATATGAGCCTACCAGCATGCGAGCTATTCGAGCCAGgtgaag--------ag---tgtcttctgtgttatgg-aattgaaacttgtattacagcttctggattgatctagtaaagggtttggggtttaggtagttttgggtgaaattt

upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgtt-agttttgtcttttgtgttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt
| || || || ||||| || |||||||| || || || ||||||||||| ||||| ||||| || || || || ||||||||||| ||  ||||||| ||||||||||| | || || |||   |||| | ||   |||       ||||||  | ||  | | |    ||  |||  ||        ||   || ||   
TTTGTGTTTATTGCCCTGGAGGACCTGATTCTGATTTTGAGTACAGTACACAGTCGTACACTGGATACGAGCCCACCAGCATGCGCGCGATTCGTGCTAGgtagggtttttctttaggttttaattttat-ttgttgtattgatctctgtttggatgatgggaaatcataggaaaaggaactaagtcttttcattaatgaa

upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ21486 (Selaginella moellendorffii), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagttttgtcttttgtgttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt
|||| ||||||||||| || || || || || |||||||| || || || ||||| ||||| || ||||||||||| |||||||| ||| |||| || |||||   | |||  |   ||| || ||| | ||   |  | | |||     || |                                              
TCTGTGTCTACTGCCCGGGAGGCCCAGATTCGGACTTCGAATATAGCACACAGTCCTACACTGGGTATGAACCAACGAGCATGCGAGCAATTCGAGCAAGgtaaattctatagt--ctttttcatttctttttttgctagcaaaaaaaaattcag---------------------------------------------

upper sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ27078 (Selaginella moellendorffii), 5'ss of exon 1
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagttttgtcttttgtgttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt
|||| ||||||||||| || || || || || |||||||| || || || ||||| ||||| || ||||||||||| |||||||| ||| |||| || |||||   | |||  |   ||| || ||| | ||   |  | | |||      | |                                              
TCTGTGTCTACTGCCCGGGAGGCCCAGATTCGGACTTCGAATATAGCACACAGTCCTACACTGGGTATGAACCAACGAGCATGCGAGCAATTCGAGCAAGgtaaattctatagt--ctttttcatttctttttttgctagcaaaaaaaaaatcag---------------------------------------------

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|7691758|gb|AW759879.1|AW759879
EST:     CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAA                         GTATAATCCATATGTCCAAGCGAAGTGCAAGATAGATCAGCTTAAGCGTTT
genomic: CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggttta ... ctggatttagGTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTT
EST: gi|193410352|gb|FK379335.1|FK379335
EST:     CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAG                         GTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTT
genomic: CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggttta ... ctggatttagGTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTT
EST: gi|193430258|gb|FK393260.1|FK393260
EST:     CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAG                         GTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTT
genomic: CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggttta ... ctggatttagGTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTT
EST: gi|7691698|gb|AW759821.1|AW759821
EST:     CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAG                         GTATAATCCATATGTTCAAGCGAGGTGCAGGATGGATCAGCTTAAGCGTTT
genomic: CAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggttta ... ctggatttagGTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCGTCTACTGCCCCGGGGGACCTGACTCCGACTTCGAGTACAGTACCCAGTCTTACACCGGTTATGAACCAACCAGCATGCGTGCAGTTCGTGCGAGgtagggtttatgttagttttgtcttttgtgttagggtaaacgaaactgtttttaagagtgaatagttgagtcaaattaatccctatattctgttgatttt

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