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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacatttccattttgccttggtaatcataaaatggttatttgtcagagacagaaatcttaggcttcttttcacctagatctccccttcacttgatgctaatttttgctgaagacttatatttcacaacttacccaactctcttacactcagcatttttattatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCAGCTTATCGGACTCCCAAGTGTGTTAAAAAGTGTGTAAGTGGAAACCAAG

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 6
gtaatacatttccattttgccttggtaatcataaaatggttatttgtcagagacagaaatcttaggcttcttttcacctagatctccccttcacttgatgctaatttttgctgaagacttatatttcacaacttacccaactct-cttacactcagcatttttattatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCAGCTTATCGGACTCCCAAGTGTGTTAAAAAGTGTGTAAGTGGAAACCAAG
                                                          ||| || | |   ||       ||| |  |    | || |  ||   ||||  |  ||   ||   |||| |    || ||  | | || |  || ||   | ||  ||  ||||||||||||||||| ||||||   | |||||||||||| ||||||||||| || |  ||||  || || |||||||| |  |||||      || ||||||| 
----------------------------------------------------------atcctatgttatgttct-----gatatttca---atttaagacttgcttttattccag---ta-gcttcata---cacacaggtatgctaatgctgagtgatgtt--tacttggcagTGTGACCCATACTTTGATGCTACTGGCTGTTCTCACCCTGGTTGTGAACCTGGATATCCCACCCCAAAGTGTGTGAGGAAGTGCACTGATGAAAACCAAC
















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|13252459|gb|BG363370.1|BG363370
EST:     CTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|192323979|gb|FK015700.1|FK015700
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|58018606|gb|CX705348.1|CX705348
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|19346536|gb|BM891416.1|BM891416
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAA                         TGTGACCCATATTTTGATCCAATTGGCTGTTCTCATCCTGG
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGG
EST: gi|120532302|gb|EH260435.1|EH260435
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTTGTGAGCC
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTT-GTGAGCC
EST: gi|151400974|gb|EV270788.1|EV270788
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|192308925|gb|FK002149.1|FK002149
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|151411964|gb|EV281775.1|EV281775
EST:     CTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCCTGGTTGTGAGC
genomic: CTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAA-GAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCC-TGGTTGTGAGC
EST: gi|8670417|gb|BE191524.1|BE191524
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|6666111|gb|AW277570.1|AW277570
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
EST: gi|10238899|gb|BE807795.1|BE807795
EST:     CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATAGGCTGTTCTCATCCTGGTTGT
genomic: CCTTATATGCATGGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGT
EST: gi|254336334|gb|GR842513.1|GR842513
EST:     GGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAG                         TGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA
genomic: GGCGATACTTAGCCCACCATGGTGTTGTCACTGAAGAGgtaatacatt ... tatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttcacaacttacccaactctcttacactcagcatttttattatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCAGCTTATCGGACTCCCAAGTGTGTTAAAAAGTGTGTAAGTGGAAACCAAG
                                      tttttatt  CT-rich tract
                                     atttttattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacatttccattttgccttggtaatcataaaatggttatttgtcagagacagaaatcttaggcttcttttcacctagatctccccttcacttgatgctaatttttgctgaagacttatatttcacaacttacccaactctcttacactcagcatttttattatgtggcagTGTGACCCATATTTTGATCAAATTGGCTGTTCTCATCCTGGTTGTGAGCCAGCTTATCGGACTCCCAAGTGTGTTAAAAAGTGTGTAAGTGGAAACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA