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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcattaagtcttttatttattatatttttggactttagttatgtgtggaggtcaattcagttctatatatattcccttttttagtaactgagaa...

Basic information

species Glycine max
transcript GLYMA06G01280.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 9
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcattaagtcttttatt-tattatatttttggactttagttatgtgtggaggtcaattcagttctatatatattcccttttttagtaactgagaa-----
|| || || |||||||| || |||||||||||||| || ||  ||||||| || |||||||| ||| | ||| |||||| |||||||||||||||||| |||||| |       |||| ||   |  ||| |   ||||   |    | |     |  | | |   ||  | |  |   |     | || ||   |||        
TCGTGCCAGATGTATCAACGCTCTGCTGATATGGGACTTGGTGTTCCATTCAACATTGCATCATATTCTCTTCTGACATACATGATTGCTCATGTTTGCGgtatgtt------atcttctaccctgctatgtgactggataatcccaaaggtctaaccttattgatgtattgttcagcgtaagactgtttgttgttgatgttgtat

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 5'ss of exon 7
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatg--ctcattaagtcttttatttattata-tttttggactttagttatgtgtggaggtcaattcag--ttctatatatattcccttttttagtaactgagaa
||||| || ||||| || || |||||||||||||| || ||  | ||||| || |||||||| ||| | ||| ||||||| |||||||| || || |||||||||  |||| |   |  | | ||||      || || |  |||  | | ||       ||||   ||    |  |  | || |   || || |||||      
TCATGCCAGATGTACCAACGCTCTGCTGATATGGGGCTCGGTGTGCCATTCAACATTGCATCATATTCTCTTCTGACATGTATGATTGCACAAGTGTGTGgtatgttctcacttgcttatctttttacaccggttattcgtttttcctaaagtcaaagcttcaaactagaacccattgcacatgctaattattcgtaaca-----

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 8
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcattaagtcttttatttattatatttttggacttta--gttatgtgtggaggtcaattcagttctatatatattcccttttttagtaactgagaa
|| || || |||||||| || ||||| || ||||| || ||  ||||||| || || ||||| ||| | ||||||||||  ||||||||||| |||||||||| | || |  |  | |   | || ||| | |    | |  |  |||   |||| |  | |||  |   ||   |   |   | | |   |||  || |  
TCCTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTTTTGACATATATGATTGCTCAAGTTTGTGgtaggttcttatatgcatcactgtaatatttctactcagtgcaacgtttattgtgcaccttaatagaaaccttcttggttgtacatgtactgtatttgtg--

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat----taagtcttttatttattatatttttggactttagttatgtgtggaggtcaattcagt-tctatatatattcccttttttagtaactgagaa
||||| |||||||| |||||||||||||| ||||| || ||  | || ||||| |||||||||||||| || || ||||||||||| |||||||||||||||||||   |     || ||    |        | |||||  |    |  |  |    ||  |  || | | |||| ||| ||       | |||  |       
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgcatttgtgacaaatccagaaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtacatgtaggcatc-----

upper sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 5'ss of exon 8
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgc--tcattaagtcttttatttattatatttttggactttagttatgt-gtggaggtcaattcagttctatatatattcccttttttagtaactgagaa-------------------------------------------------------------
|| ||||||||||||||||| |||||||||||||| || ||  | |||||||| ||||| ||||||||  | |||||||||||||||||||||||||||||||||   | |||    || | |     || |  |||| | |      || | ||     |   | ||    | ||| |  |  || |  | | |  ||  |                                                              
TCCTGTCAAATGTATCAGCGCTCTGCTGATATGGGTCTTGGTGTGCCATTTAACATTGCTTCTTATGCTTTATTGACATGCATGATTGCTCATGTTTGTGgtatgtatttatttctactatgagaatgtaaacctttgaaataagaggatctagttataatttctccatagttctatttcatttctgtcctggca-ttggcatcatgagttatcaatcatctacacccttttaaaaatccctctacattaatttgcctgtacag

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|208272311|gb|GE073181.1|GE073181
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCCCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
EST: gi|22524702|gb|BU083513.1|BU083513
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
EST: gi|192311470|gb|FK005201.1|FK005201
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
EST: gi|193366029|gb|FK333334.1|FK333334
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
EST: gi|192311469|gb|FK005200.1|FK005200
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
EST: gi|193555347|gb|FK511032.1|FK511032
EST:     TGCATGATTGCTTCTATGTTTGTG                         ATCTCATTCCTGGTGATCTTATTCATGTTATTGGGGATGCTCATATTTAC
genomic: TGCATGATTGC-TC-ATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTAC
EST: gi|193533234|gb|FK493712.1|FK493712
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
EST: gi|207838425|gb|GD811963.1|GD811963
EST:     TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG                         ATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcat ... ttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgctcattaagtcttttatttattatatttttggactttagttatgtgtggaggtcaattcagttctatatatattcccttttttagtaactgagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggagg