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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattttgaagtgctattttttgaaatctattgtttatcagctgaaattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG

Basic information

species Glycine max
transcript GLYMA08G23930.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
--taattttgaagtgctattttttgaaatctattgtttatcagctgaaattg-tcaatttgttgtttaattagctgaagttttctgcttttttgtcccat----cagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
  || || |    |||||  | ||     ||||  ||    |||  |||| | ||   |   | | |||       | | ||| |   ||| |   | ||    ||| ||||||||||||||||||  ||||||||  |||||||||| ||||  |||||||| || || || ||| ||||||||||||||||||||||||||||||
tttatttcttgtctgctacgtctt-----ctataatta--tagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG

upper sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
-taattttgaagtgcta--ttttttgaaatctattgtttatcagctgaaattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
 ||||  |     ||||  | |||||  |||  | ||| |     |   |||| || ||   | |||  | |         |   | ||  || |   | ||| |||||||||| ||||||||||| |||||  ||||||| ||||| |  || ||||| || || ||| || |||||  |||||| ||||| ||||||||||
ataatgcttgtcagctaactgttttgtgatc-gtagttgaatgagttttattggca-ttcaatattttgtcaaggttctactaaaggttccttattt-accagATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG

upper sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
taattttgaagtgctattttttgaaatctattgttt-atcagctgaaattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatc----agGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
 | ||||    |  | |    ||||||  || | || |     || | ||||| ||  |||  |||  | | |  |   |     |||| |            || | ||||| || ||||||||||||||||||  |||| | ||||| || || || ||||| ||||||||  ||||||||||||| ||||||||||||||||
-agttttt---ttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagtt-cttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG

upper sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
taattttgaagtgctattttttgaaatctattgtttatcagctgaaattgtcaatttgttgtttaattagctgaagttt--tctgcttttttgtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
 | |  | || |  |   |   ||| || | | |   |  |   |  |  | |  ||  | || || |   | ||  |     || | |  |      | || | ||||| || ||||||||||| ||||||  |||||||||||| ||||| |||||||| ||||||||||||||||||||||| || |||||||||||||
-actgctaaaattatgactcgcgaa-tccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtttttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG

upper sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 1
-taattttgaagtgctattttttgaaatctattgtttatcagctgaaattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatc--agGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
    | || |  ||   |    |||||| ||||          ||       ||     |   ||||| |    ||  ||  |  ||  ||||   ||   |||||||||| || ||||| || ||||||||||||||||||||||| || || || ||||| || ||||| |||||||| ||||| ||||| ||||||||||
actctgttcatctgtgttcccatgaaatatatttgcctgagtgtgttgcaaacaccacatgacttaatgaa---aaccttggtaattgcttgtttaattgaagGTTATGGCGGTAAAGAAAAACATTGAAGATGTACAAGGAAAAGACAACTATCCGTGTGGGCAACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATG

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|4307032|gb|AI443989.1|AI443989
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298198982|gb|HO042345.1|HO042345
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|192332023|gb|FK024539.1|FK024539
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|208326137|gb|GE121079.1|GE121079
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|208326137|gb|GE121079.1|GE121079
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|16348403|gb|BI973998.1|BI973998
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298178394|gb|HO024129.1|HO024129
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|16105282|gb|BI893022.1|BI893022
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTATTTTGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|151410032|gb|EV279840.1|EV279840
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|208311677|gb|GE109011.1|GE109011
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|208078931|gb|GD876547.1|GD876547
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATNTTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298171945|gb|HO021537.1|HO021537
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|27446142|gb|CA953265.1|CA953265
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298196834|gb|HO041577.1|HO041577
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|298179084|gb|HO027555.1|HO027555
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST: gi|120495849|gb|EH224016.1|EH224016
EST:     AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACT                         GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGATACTgtcagtaatc ... gtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
               gtttaat  putative branch site (score: 4)
                               ttttctgcttttttgt  putative PPT
       aatttgttgtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattttgaagtgctattttttgaaatctattgtttatcagctgaaattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG