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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag

Basic information

species Glycine max
transcript GLYMA08G26180.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaa-tggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag
||| ||||| |||||||| || ||||||||||| ||  | ||||||||||| |||||||| || ||||||||||| ||||| || |||||||| |||||||| | ||  | ||||   | ||   | |  |  ||    ||   |  ||| |  ||  | |  ||| |     ||    |  | |||||  |||    ||
ATGCAATGTTAAGATTGCAGACTTTGGCTTGAGTAATGTTATGCGTGATGGTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacatggcgaaaattattgttga-ggatatatatatat-tgtctcttgtgattcatatttcttggttacactttttcatttttcacag
||| ||||| |||||||| ||||||||||| || || || ||||||||||| ||||||||||| || |||||||| ||||| || |||||||| |||||||| |    | | |||  |  | |  |   |  || | || |  || || || | |  ||||  ||  | |  | |  ||   | ||| | |          
ATGCAATGTTAAGATTGCCGATTTTGGCTTAAGTAATATTATGCGTGATGGTCACTTTCTTAAGACGAGTTGTGGTAGCCCGAATTATGCAGCACCTGAGgtatcatctagcataatttacaattagcgtccttcatggttgcatttacatatataacttgccatg-acacgtttctgtcttattttcttag---------

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgt-------ttgtaatgg----aatacatggcgaaaatt-att-gttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag
||| ||||| |||||||| ||||||||||| || ||  | ||||| ||||| || ||||| || ||||||||||| ||||| || ||||| |||||||||||        | |||| |    || | ||   ||  |   ||| | | || ||     ||| |  |  |   |  ||   |     |      |   ||| |||||   |||
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagta-cagtatccttttattttctgcag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctc-ttgtgattcatatttcttggttacactttttcatttttcacag
||| ||||| |||||||||||||||||| |||||||||| ||||| ||||| || ||| | || |||||||||||||| || || ||||| ||||| |||||  ||  |  |   |   |         |   ||||||    ||||  | | ||  ||   | | |||  |  | ||     | | | | || |  |||
ATGCAATGTAAAGATTGCTGATTTTGGCCTGAGCAACATAATGCGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGTCCAAATTATGCCGCTCCAGAGgtaagtgcttcagccctcag--------gtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag
 |||||| | |||||||| || ||||| ||||| ||  | ||||| ||||| || ||||| || || |||||||||||||| ||||| || ||||| ||||| | || |  | || |       |||| || || |     ||| |  | | | ||| ||   || |||   |   |||    ||     || |   ||
GTGTAATATTAAGATTGCAGACTTTGGGTTGAGTAATGTTATGCGGGATGGTCATTTTCTAAAGACGAGTTGTGGAAGCCCCAACTACGCTGCTCCCGAGgtatatagtttagtaaagttactgaattgtttttca---cctatgtg-actatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgt---------------ttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttca--cag---------------
||| ||||| ||||||||||||||||| || || || |||||| | ||||| || ||| | || ||||||||||||||||| || ||||| || || |||||               || ||||  || |||   |  || || | ||||||     |  || | |   |  |   ||       |  |||||  | ||| | |  ||  |   ||               
ATGCAATGTGAAGATTGCTGATTTTGGTTTAAGTAATATCATGAGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGCCCAAATTATGCTGCCCCAGAGgtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagttacaatactttctaatatatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 5'ss of exon 3
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag
 || ||||| |||||||| || ||||||||||| || |||||||| ||||| |||||||| ||||| || |||||||| || |||||||| ||||| |||||  |    |   | | |        ||  | | ||     | |   | |                                                 
GTGCAATGTGAAGATTGCGGACTTTGGCTTGAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgactttctt------ttttcctctagaaagccttttcctttcag----------------------------------------------

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|308099103|gb|HO760944.1|HO760944
EST:     GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
EST: gi|208210675|gb|GE011736.1|GE011736
EST:     GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
EST: gi|209726300|gb|BW659613.1|BW659613
EST:     GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
EST: gi|17519479|gb|BM188521.1|BM188521
EST:     GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
EST: gi|208161501|gb|GD959685.1|GD959685
EST:     GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAACTGTATGCTGGACCTGAA
genomic: GCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAA
EST: gi|193495997|gb|FK461937.1|FK461937
EST:     TTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: TTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacatggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC