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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgatgaatagattcactttctctgtcttctctccatatttttgagcatgtatggactgattacagtgacaaaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA

Basic information

species Glycine max
transcript GLYMA06G18730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G18730.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 5
gtatattgatgaatagattcactttctctgtcttctctccatatttttgagcatgtatggactgattacagtgacaaaaattt-cagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA
     ||  ||  |   | || ||  | | | |       ||  ||||  |    |||   || ||     ||| | | ||   |||||||| || || || ||| | ||||| || || |||||||||||||| |||||||| || | |||||| |||||||||||||| ||||| ||| | ||||
----gtttctg--ttactgcagttcatatttgtcaatataattcttttttgtcaatatttgctaatcc---tgaaatatatccacagTTGTACAGCACAGTGACATTGAGGCATGGAGAAAAGAAGCATTACAATCATAAAGTAGACGTTTATAGCTTTGCAATTGTGTTATGGGAACTCCTTCACA

upper sequence: GLYMA06G18730.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G165231_T01 (Zea mays), 3'ss of exon 4
gtatattgatgaatagattcactttctctgtcttctc-tccatatttttgagcatgtatggactgattacagtgacaaaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA
     ||  | | |  || ||  || |  || |     ||| || ||||  | ||   |    | |     |      |||   |||||||| || || || ||||| ||||| || || ||||||||||||||||| ||||| ||||  || || |||||||||||||||||||| ||| | ||||
----gtttct-actgcatccatatttttagtttctgagtccttaattttctgtattattaatgtaacctgggaattctaaa---cagTTGTACAGCACAGTAACACTGAGGCATGGAGAAAAGAAGCATTACAACCACAAAGTAGATGTCTACAGCTTTGCAATTGTGTTGTGGGAACTCCTCCACA

upper sequence: GLYMA06G18730.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 4
--gtatattgatgaatagattcactttctctgtcttctctccatatttttgagcatgtatggactgattacagtgacaaaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA
     | || |   |||||   | ||| |   | |  | | | | | ||||   |  ||  |||  ||    |||   || ||| |||||||| || || || || ||  |    || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||  | |||||||| |||||||
gttcttctttacttatagacata-tttgttcatttcttgtgcttctctttgc-tacttaaagac-aatcttggtg--gaatattacagTTGTACAGCACGGTAACTCTTCGATTGGGAGAGAAGAAGCACTACAATCATAAAGTCGACGCCTATAGCTTTGCAATAGTTCTTTGGGAGCTTTTACACA

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|18720447|gb|BM523256.1|BM523256
EST:     CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
EST: gi|6566830|gb|AW234462.1|AW234462
EST:     CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
EST: gi|6725443|gb|AW309842.1|AW309842
EST:     GGGAAC-TACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGT-ACACTTAA-GCAAGGGGAGAAGAAGCA-TACAACCA
genomic: GGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACAC-TAAGGCAAGGGGAGAAGAAGCATTACAACCA
EST: gi|19936237|gb|BQ080780.1|BQ080780
EST:     CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
EST: gi|31471429|gb|CD413457.1|CD413457
EST:     CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
EST: gi|7638929|gb|AW733194.1|AW733194
EST:     CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
EST: gi|192311809|gb|FK003614.1|FK003614
EST:     CTGAGATGATGACTGCTGAGGCGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAGGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT
EST: gi|192312935|gb|FK003615.1|FK003615
EST:     CTGAGATGATGACTGCTGAGGCGGGAACTTACCGTTGGATGGCTCCAGAG                         TTGTATAGTACTGTCACACTAAGGCAGGGGGAGAAGAAGCATTACAACCAT
genomic: CTGAGATGATGACTGCTGAGACGGGAACTTACCGTTGGATGGCTCCAGAGgtatattgat ... aaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctctccatatttttgagcatgtatggactgattacagtgacaaaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA
                            gactgat  putative branch site (score: 3)
         atatttttga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattgatgaatagattcactttctctgtcttctctccatatttttgagcatgtatggactgattacagtgacaaaaatttcagTTGTATAGTACTGTCACACTAAGGCAAGGGGAGAAGAAGCATTACAACCATAAAGTTGATGCTTATAGTTTTGCAATTGTGTTGTGGGAGCTCTTACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT