Sequence
atgc intronic sequence ATGC exonic sequence...cctttcttggctatatgaagtcaatttcactattttctgttcatatattagtatatcatctctaatgctttatcttgtgcttatatgcaatggaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCAACAGTCTCTTCAACAATACAGGGCTATTTGGCATATATGCAAGCACA
Basic information
species | Glycine max |
transcript | GLYMA13G43000.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------------------cctttcttggctatatgaagtcaatt--tcactattttctgttcatatattagtatatcatctctaatgctttatcttgtgcttatatgcaatg-gaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCAACAGTCTCTTCAACAATACAGGGCTATTTGGCATATATGCAAGCACA
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gtaagttttacatatggctactggttttcttgtagcttaccttgatcatttgggttattgttatttattattgttggactttatagctgcttggatttcctgtgttgttgcattaatgttgattgagtatatatttctaaatttctgctaa-gtttaactcgcttgtttcacccattttgaacacagATCTTCGTGTCTTGAATGAGTATCAACAACTTCAATCTTTCTCTGCATTCAACAATATCTTCAACAATACTAGAATTTTTGGCATTTATGCTAGCACT
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------------------------------------------cctttcttggctatatgaagt-caatttcactattttctgttcatatattagtatatcatctctaatgctttatcttgtgcttatatgcaatggaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCAACAGTCTCTTCAACAATACAGGGCTATTTGGCATATATGCAAGCACA
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gtaagttttacatatggctactggttttcttgtagcttaccttgatcatttgggttatggttatttattattgttggactttatagctgcttggattcctgtgttgttgcattaatgttgactgagtatatatttctaaatttctgctaagtttaactcgtttgtttaacccattttgaacacagATCTTCGTGTCTTGAATGAGTATCAACAGCTTCAATCTTTCTCTGCATTCAACAATATCTTCAACAATACTGGAATTTTTGGCATTTATGCTAGCACTMapped 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|8402432|gb|BE058066.1|BE058066EST: TGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT TTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCA
genomic: TGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGTgtaagtttta ... tggaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCA
EST:
gi|18041237|gb|BM309531.1|BM309531EST: GGGTCGTTCTCTGCTGGAGGGCCTGGAAAAAGGATGCATTTCA-GGCTGT TTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCT
genomic: GGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATT-CAAGGCTGTgtaagtttta ... tggaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattagtatatcatctctaatgctttatcttgtgcttatatgcaatggaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCAACAGTCTCTTCAACAATACAGGGCTATTTGGCATATATGCAAGCACA
ctctaat putative branch site (score: 3)
tatatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctttcttggctatatgaagtcaatttcactattttctgttcatatattagtatatcatctctaatgctttatcttgtgcttatatgcaatggaatccagTTCTTCGTGTCTTGAATGAACATCAACAGATTCATTCTTTTTCTGCATTCAACAGTCTCTTCAACAATACAGGGCTATTTGGCATATATGCAAGCACA
- - - - - - -tatgaag
- - - - - - - - - - - - - - - - - ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcaa