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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC

Basic information

species Glycine max
transcript GLYMA13G03430.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 7
------ac-ttcagat-ttttgttatatgtcttaggctcttagctttatcttatgaaac--aataaatttgtag-------ctcac---tcagtctccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
      || | || || ||||   |    | |     ||||   ||| | ||  ||||    |||    ||| |        |||    |||   | ||      |  || |  |  |||||||||||| || ||||||||| ||||||| || ||||||||||||||||| || || || || ||||| ||||||||||| ||||||||  | ||||||
gtatttacatacatatattttcacagccatgtggaattcttttttttttttttagaaaatggatagccatgtggaaatgtcttcagaaatcatcatgctgatgctatgttcatttcccagCTTGGTGAAGTTCTTGACACCTTCATCTGGGCTTCAAGGATACTGGGATCCATACCCGATCGACATGGAATTTCGACCACCATGCATGGTGTTGTCAACC

upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 7
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttg-cagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
        | |||   |||  | | |       |    |  |   |||||   |   ||   |  ||| |||  ||  |   ||  |||     ||| |||||||||||| || ||||||||||||||||| || ||||| ||||||||||| || || || || |||||||||||||| || ||||||||  | ||||||
-------gtatttac-atacatatcaactaaggacaactggccattgaaaattt---ttcacaaatca-tcatgctgatgctat--attcatctttgtcagCTTGGTGAAGTTCTTGACACCTGCATCTGGGCTCCAAGGGTACTGGGATCCTTACCCCATCGACATGGAGTTTCGACCGCCATGCATGGTCTTGTCAACC

upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G038487_T01 (Zea mays), 3'ss of exon 7
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagc-tcactcagtctccttgcatgaatttgaacttg-cagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
      |  | |   | |   ||| |   | | |    || || | |||   | |  |   ||   ||||   |    ||    |    |||    || ||| |||||||| || || |||||||| ||||| || ||||| ||||||||||| || || || || |||||||| ||||| || || |||||  | || |||
------gtatgtacctttgcatctcac-ttgtgaaaactaactgacgaatatacacttccataatatcaccatggtggctgatgtcgtgttgtttctgtcagTTTGGTGAAGTTCTTAACACCTGCGTCTGGGCTCCAAGGGTACTGGGATCCTTACCCGATCGACATGGAGTTCCGACCGCCATGTATGGTCTTGTCGACC

upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 7
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
                 | | | |||  |||| |   |||   | |  |    |||  |   |  |   | |  ||   ||      ||||    ||||| |||||||| ||||| |||||| | || || || ||||||||||||||||| ||||| || |||||||| |||  |||||| || || ||  |||| || 
----------------gtttcttttaa-ctctca---ttactctgttcagtgctaagatgaaacttggtttaagctttctgtt----tttggtactgcagTTTGGTGAAGTTTTTAACACCTACCTCGGGTCTCCAAGGATACTGGGATCCATATCCAATCGATATGGAATTTAAACCACCGTGTATTGTTTTATCGACA

upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtag--ctcactcagtct---ccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
                        |  | || |  |  |||   ||   |   | | |||| ||  | ||  |||  |     ||| || | | |||| |  ||||||||| || || ||||||||||||||||| || |||||||||||||||||||| || || |||||||| |||||||||||||| ||||| || ||||||
-----------------------gtttgttcctgtcaatattgcatttcatggttattttggagggcccatccagcttaagttttgtatta-tctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC

upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ15257 (Selaginella moellendorffii), 3'ss of exon 6
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
                                                  |  | |   |    |||  |  || || |  ||     |||    | |||||  ||||| ||    ||||||| |      || |  || ||||||||||| ||||| ||||||||||||||| | | ||| |||||||| || || || 
-----------------------------------------------gttcgtttatcgttggtctcttttcgtgtcttaacaattccttgg--ctccagCTCCGTGAAGTTCCAAACACCTGTAGAGACTCTACGTGGCTACTGGGATCCATATCCCATTGATATGGAGTTTAGGCGACCGTGCATGGTTCTCTCGACG

upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ08372 (Selaginella moellendorffii), 3'ss of exon 6
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttg----cagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
                                                     |   ||| | | ||  ||  | | | ||  | || |    ||||    |||||  ||||| ||    ||||||| |      ||||  || ||||||||||| ||||| ||||||||||||||| | | ||| |||||||| || || || 
----------------------------------------------------gttcgtttatcgttc-ttctcttttcgtgtcttaactattccttggctccagCTCCGTGAAGTTCAAAACACCTGTAGAGACTCTGCGTGGCTACTGGGATCCATATCCCATTGATATGGAGTTTAGGCGACCGTGCATGGTTCTCTCGACG

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|11413508|gb|BF425519.1|BF425519
EST:     GCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAG                         CTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCC
genomic: GCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAGgtttgtttgg ... gaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCC
EST: gi|13125056|gb|BG315599.1|BG315599
EST:     GCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAG                         CTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCC
genomic: GCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAGgtttgtttgg ... gaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCC
EST: gi|22524453|gb|BU083264.1|BU083264
EST:     GCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAG                         CTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCC
genomic: GCCCCTTTTACTCACACCTCAACATTTGCTAAGGGATGGAGTGTTCCCAGgtttgtttgg ... gaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC
                 agctcac  putative branch site (score: 3)
      aataaatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttcagatttttgttatatgtcttaggctcttagctttatcttatgaaacaataaatttgtagctcactcagtctccttgcatgaatttgaacttgcagCTTGGTGAATTTTTTGACACCTGCATCTGGCCTGCAAGGATACTGGGATCCCTATCCTATTGATATGGAGTTTCGACCACCTTGCATGGTACTATCAACC

- - - - - - - - - - - - - - - - - - - - - - - gaaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcactca