Sequence
atgc intronic sequence ATGC exonic sequencegttagtgacaaggacagtattatactgtttttttatttcttggatttcataactctttcaatctctgtttgtttaaactattatgctgattatgtggtttttttaatggaatttaaccttgaatattggtatttacattttctattagtctttcttgacatgcattaatgatcctttcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGATTGTTCTTTTCTTGATACTTGCCGACACATGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G03690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03690.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g45110.1 (Oryza sativa), 3'ss of exon 2
gttagtgacaaggacagtattatactgtttttttatttcttggatttcataactctttcaatctctgtttgtttaaactattatgctgattatgtggtttttttaatggaatttaaccttgaatattggtatttacattttctattagtctttcttgacatgcattaatgatcctttcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGATTGTTCTTTTCTTGATACTTGCCGACACATGAAG
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------------------------------------------------------------------------------tttttccttgaatacttgaatagcttt-tgttatctggtctttta----gctgttcatggtaacaactaatctgga--agtaactgtttatatttcattc-tgagcagGTCCATTTCCGCCGTATTATTGCTCCTCATACTGATACAAACCTAGGAGATTGTTCTTTTCTCGACACTTGCCGTCACACAAAG
upper sequence: GLYMA16G03690.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G10760.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtgacaaggacagtattatactgtttttttatttcttggatttcataactctttcaatctctgtttgtttaaactattatgctgattatgtggtttttttaatggaatttaaccttgaatattggtatttacatt--ttctattagtctttcttgacatgcattaatgatcctttcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGATTGTTCTTTTCTTGATACTTGCCGACACATGAAG
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-------------------------------------------------------------------------------------ttgtttgt-tattttgtgaggtttatattgatctcctgctatggtgtctatgttgctttgctgaaatctacttagtttttatgaat--tctgtatactttcagAGACATTTCCGTCGACTAATCGCTTCACATACTGACGTTAGCCTAGGAGATTGTTCCTTTCTCGATACTTGTCGTCACATGAAG
upper sequence: GLYMA16G03690.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g02400.t01 (Vitis vinifera), 3'ss of exon 2
gttagtgacaaggacagtattatactgtttttttatttcttggatttcataactctttcaatctctgtttgtttaaactattatgctgattatgtggtttttttaatggaatttaaccttgaatattggtatttacattttctattagtctttcttgacatgcattaatgatcctttcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGATTGTTCTTTTCTTGATACTTGCCGACACATGAAG
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------------------------------------------------------------------------------tat-aagctgtgtgtcctcatgttctaagcctatatagcctttgtt--tcacttttac----tctaattagatattttgtcttac-tgaagcatatcactaatttcagGTCCATTTTCGGCGTATAATTGCTCCGCATACTGACATCAACTTAGGGGACTGTTCTTTTCTAGATACTTGCCGTCATATGAAGMapped 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|18040168|gb|BM308462.1|BM308462EST: CAAAAGAGGATTGCCGACGTCAAACTGGTTCCTTTATAGCATGTGATAAG GTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGAT
genomic: CAAAAGAGGATTGCCGACGTCAAACTGGTTCCTTTATAGCATGTGATAAGgttagtgaca ... tcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGAT
EST:
gi|254318349|gb|GR832517.1|GR832517EST: CAAAAGAGGATTGCCGACGTCAAACTGGTTCCTTTATAGCATGTGATAAG GTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAAATTTAGGAGA
genomic: CAAAAGAGGATTGCCGACGTCAAACTGGTTCCTTTATAGCATGTGATAAGgttagtgaca ... tcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAA-TTTAGGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacattttctattagtctttcttgacatgcattaatgatcctttcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGATTGTTCTTTTCTTGATACTTGCCGACACATGAAG
cattaat putative branch site (score: 3)
tcctttcctttgc putative PPT
attttctatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgacaaggacagtattatactgtttttttatttcttggatttcataactctttcaatctctgtttgtttaaactattatgctgattatgtggtttttttaatggaatttaaccttgaatattggtatttacattttctattagtctttcttgacatgcattaatgatcctttcctttgcagGTTCATTTTAGAAGGATCATTGCTCCTCATACTGACATCAATTTAGGAGATTGTTCTTTTCTTGATACTTGCCGACACATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT