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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA

Basic information

species Glycine max
transcript GLYMA08G12120.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 3
gtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA
|||      ||| |  |||      | ||  | | |     |   | | ||| |||    |||    ||  | || ||||  |||||||||||||||||||||||||||| || ||||||||||| ||  ||||| |  | |||||||| ||||| || ||  | ||| | || || || || |
gtacaagaggaaatatttt------tgaaggttttcgggccagcat-tcttgctcaaa-gttttgcaatcttattgtttc--agGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATACTCATGAATGCAACTGACAAATCAAATAGAATGTTGCGGGCCAAATCGA

upper sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------gtattttgtgaacttctttgttcaatcaacatatgcaatttatttt--cttttgatcactcatttaattattatgttctt-tctt--agGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA
                                            |      |  |  ||   | ||  |   |  |      || ||      || | ||      || |||| |  ||| ||| ||||  |||| |||||| ||||||| |||||||| || |||||||| ||||||||||| ||  | |||||||| || ||||| ||  | ||||||||||| ||||| |
gtaatttgtccatgtataagttagcttaatttcttatagggggagggggacgcaacattaccttttatacttatcttgatggttaatgagagtttataatattgtgttaaattttggtgtacttgtcttgcagGAGCACTTCAAAAAATACTATGATGCAGTGATGCCATACCTGAAAGCTATTTTAATGAATGCAACTGATAAGTCCAATAGGATGCTTCGTGCCAAGTCTA

upper sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 3
gtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA
|||  |   ||| | |   ||||||||    |    ||  || |    |   || | |  ||| | | ||||    ||  | |||||||||||||||||||||||||||| ||||||||||| || || |||||  |  | |||||||| || || || ||| | ||| | ||||| || ||||
gtagatcaggaaataca--gttcaatccttcttgttaacatagtaatctaacataaat--tttcaatcttat----ttattcagGAACACTTCCAAAAATATTATGATGCAGTAATGCCATACCTCAAGGCTATTCTCATGAATGCAACTGATAAATCCAACAGAATGTTGCGTGCCAAATCCA

upper sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattttgtgaacttctttgttcaatcaac-atatgcaatttatttt-cttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA
||||||    |     | ||||  ||| |   | | |  |  ||    || ||||||  | | |  |  || || |   ||  ||||||||||| ||||| || |||||| |||| ||||| ||||| ||| |||| ||| | |||||||| ||||||||||| || ||||||||||| || ||||
gtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatc--taagtctaacataatctaaatttgtagGAACACTTTCAAAAGTACTATGATACTGTCATGCCTTATCTCAAAACTATTTTGATGAATGCAACTGACAAGTCTAAGCGGATGCTTCGTGCCAAATCCA

upper sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 4
gtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA
       ||    |   || |  |||   | |     ||   |||  | |  || |      |||   || ||    |   |||||||| ||||||||||| |||||||| || ||||| || || ||||| |||||| | ||||| || |||||||||||||| ||||||||||| ||  |||
-------gtattatatattttaaaatatgcttccattatggttttcttataaatgagcagcctaacacttttgagtatcaatagGAACATTTCCAAAAATACTATGATGCAGTTATGCCTTACCTAAAAGCAATATTGATGAATGCCACTGACAAGTCTAACCGCATGCTTCGTGCCAAAGCCA

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|20812511|gb|BQ296989.1|BQ296989
EST:     TGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCTGTAATGCCATACCTGAAGGCTATA
genomic: TGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtg ... tctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgcaatttattttcttttgatcactcatttaattattatgttctttcttagGAACACTTCCAAAAATATTATGATGCTGTAATGCCATATCTGAAAGCTATATTGGTTAATGCAACCGACAAGTCTAACCGTATGCTTCGTGCTAAGTCCA
                              atttaat  putative branch site (score: 4)
                                       ttatgttctttctt  putative PPT
       aatttattttcttttg  TA-rich tract