Sequence
atgc intronic sequence ATGC exonic sequence...catgaatttctgtaattttttaaagtttatgcatagtataaattatagtttgtgatttgtgaaacaatctctcctagtctgatcactacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT
Basic information
species | Glycine max |
transcript | GLYMA08G01880.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
catgaatttctgtaattttttaaagtttatg-catagtataaattatagtttgtgatttgtgaaacaatctctcctagtctgatcactacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT
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-gtgaggcagtgaattctatccattcttctgatacctcgttttccttcatccttcattagttggagaat-tagatgaacatggatttta-attttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------catgaatttctgtaattttttaaagtttatgcatagtataaattatagtttgtgatt-tgtgaaacaatctctcctagtctgatca---ctacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT------------------------
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gtaagtcagatcaccttacattgttggtttggttatcctaggctatcattcattactcacccccaatgaatctcatctgttttagtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCATGTGAAATTGGCAGATTTTGGAATGGCAAAGCATGTAAGAGTATTCACATGCATTTTT
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------catgaatttctgtaattttttaaagtttatgcatagtataaattata-gtttgtgatttgtgaaacaatctctcctagtctgatca---ctacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT
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gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCATMapped 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|9899677|gb|BE608645.1|BE608645EST: CAA-TTCTATTAGGACTNGCGTATTTGCACACCAAGAACACTGTTCACAG GGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAAAT
genomic: CAAATTCTATTAGGACTTGCGTATTTGCACACCAAGAACACTGTTCACAGgttagtttgg ... ttctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAA-T
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttgtgatttgtgaaacaatctctcctagtctgatcactacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT
gtctgat putative branch site (score: 4)
aaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgaatttctgtaattttttaaagtttatgcatagtataaattatagtttgtgatttgtgaaacaatctctcctagtctgatcactacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
catgaat
- - - -ttctgta
- - - - - - - - - - - - - -tatgcat
- - - - - - - - - - - - - - - - - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaca