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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttcttttcttgcttttgaattttgggtattttgcccggtttggcaattatgttatgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC

Basic information

species Glycine max
transcript GLYMA09G01800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
ttatttcttttcttgcttttgaatt--ttgggtattttgcccggtttggcaattatgttatgattgg----atgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
     ||  || ||| ||   || |  ||   | ||||   ||  |||  |   |||  |||| |      ||   |||   || | || || | |||  || ||| || |||||||||||||| || || || || || || || || |||||||||||| | |||||||| || || ||||||||||||||||| ||||| || 
---gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatgg-atgactcttctcattgaaacttttggtgatctcttggta--tttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT

upper sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g30150.3 (Oryza sativa), 3'ss of exon 2
ttatttcttttcttgcttttgaattttgggtattttgcccggtttggcaattatgttatgattggatgctaaccactgct-aatttcct--tgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
 | ||| || ||  |  ||||     |   | ||            |   |||||  |  |||       |||   | || ||| || |  |||  ||| ||| || ||||| |||||||| || || || |||||||| || || |||||||| ||  | |||||||| || ||||||||||||||||| |||||||| |||
ctgtttgttatca-gtctttgccaaatcaatcttcaatataaaaaagt--ttatgcaagcatttagcttaaactggtactcaatctcttgatgtttctttcagGTTCTATGTAGCAGAGGTTCTCCTAGCGTTGGAGTACCTGCATATGCTTGGTATCATATACCGTGATCTGAAGCCAGAAAATGTCCTAGTTCGGGAGGAC

upper sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G026065_T01 (Zea mays), 3'ss of exon 2
ttatttcttttcttgcttttgaatt---ttgggtattttgcccggtttggcaattatg--ttatgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
    ||  |  | |  || | || |   || |   | ||  | |  ||    |  | |  ||   |||   ||  |   | |    | | |||||    || ||| || |||||||||||||| || || || ||||| || || || |||||||||||| | |||||||| ||||| |||||||||||||| |||||||| || 
----tttctgacctatttataaactagatttgtgctattatctgtcttcattaaaacgactttaaattatttggcattgattatctaataccttgatgttt-cagGTTCTATGTGGCAGAGGTACTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTTAAACCAGAAAATGTCCTCGTTCGGGAAGAT

upper sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G464985_T01 (Zea mays), 3'ss of exon 2
---ttatttcttttct-tgcttttgaattttgggtattttgcccggtttggcaattatgttatgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
    || |  | | || |  || |  ||||  | ||||||  | |  ||    |  ||| | | |    ||  |  |     ||   |  ||||    || ||| || || || || ||||| || || || ||||| || || || |||||||||||| | |||||||| || || |||||||||||||| |||||||| || 
tggatactcttgtgctatttttatagatttgtgctatttt--ctgtcttcattaaaatgatttcaacttat-ttggcgctgactgggtatcttgatgttt-cagGTTCTACGTAGCTGAGGTGCTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTCAAACCAGAAAATGTCCTCGTTCGGGAAGAT

upper sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
lower sequence: AC217842.3_FGT001 (Zea mays), 3'ss of exon 1
ttatttcttttcttgcttttgaattttgggtattttgcccggtttggcaattatgttatgattggat--gctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
 |||||    |  |    |    |  | |  || |     |     ||||  | |   | ||   ||     |||   || | |  ||     ||  ||||| |||||||| |||||||| || || ||| |||| || || ||||||||||| ||  | ||||||||| | |||||||| ||||| |||||  |||| || 
atatttagcatgataggctgccctgattgtcatgtcatttgcaactgcaagaa-gccttaatcaaatctatgaacttatgttgacatcaaaa-aatatgcagGTTTTATGTAGCAGAGGTGCTTCTTGCTCTGGAATACCTGCACATGCTTGGTATCATATACCGTGACTTAAAGCCAGAGAATGTTCTTGTGAGGGAAGAT

upper sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
-ttatttcttttcttgcttttgaattttgggtattttgcccggtttggcaattatgtt-atgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
 |||||           | || |||      |      |    |||  |  | |  ||  |  ||| |   | |       |  ||| | | | || |||||||||||||| |||||||||||  | ||| | || || || ||||||||||||||||||||||| || |||||||| |||||||| || ||  ||||||||
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaatttgattgtaatt--tttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC

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|24205771|gb|BU965024.1|BU965024
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
EST: gi|20498703|gb|BQ273633.1|BQ273633
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
EST: gi|207726276|gb|GD704644.1|GD704644
EST:     AGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: AGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
EST: gi|7685926|gb|AW756574.1|AW756574
EST:     ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAA                         ATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG
genomic: ACTCTTAGGCAGAAGCAACCAGGGAAGCATTTTCCTGAGCAGGCAGTAAAgtatgtttta ... taacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaattatgttatgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
                                     tttccttgt  CT-rich tract
     ttatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttcttttcttgcttttgaattttgggtattttgcccggtttggcaattatgttatgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC

- - - - -ttcttgc
- - - - - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgct