Sequence
atgc intronic sequence ATGC exonic sequence...atatatcagcagcagcaggtcactcaagtgatttcatttattttctccatctgtctttaggaacttcgtactagttaatattgtttttattttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCTGATGGCTCTTGGTATGGATACCGTGAAGTGGAAAAGCTGGCATCACTTT
Basic information
species | Glycine max |
transcript | GLYMA09G00460.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G00460.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g45860.1 (Oryza sativa), 3'ss of exon 11
atatatcagcagcagcaggtcact-caagtgatttcatttattttctccatctg---tctttaggaacttcgtactagttaatattgtttt---tattttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCTGATGGCTCTTGGTATGGATACCGTGAAGTGGAAAAGCTGGCATCACTTT
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-------tataagaacaagccattatgaataagatattctgaagtgcccacttgaattctgctagctctctgcacttatctattcttttctatgtattatgttttagGTGGAAGGTCTGAAAATGGGCCCTACAATCACATTCAATTTGAAAAGAGAAGATGGCTCTTGGTTTGGATACCGTGAGGTGGAGAAGCTTGCTTCCTTGT
upper sequence: GLYMA09G00460.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G16540.1 (Arabidopsis thaliana), 3'ss of exon 10
atatatcagcagcagcaggtcactcaagtgatttc--atttattttctccatctgtctttaggaacttcgtactagttaatattgtttttattttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCTGATGGCTCTTGGTATGGATACCGTGAAGTGGAAAAGCTGGCATCACTTT
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atatttgaaaaatatcatatca-tcatttactttcgaagtcacataaattacttcttcgtgtggccatagtttttgatt-cattctatgttttatgtttcagTTATCTTCACATAAATCAGGCCCAACGGTTACATTCAACTTGAAAAGACCTGATGGCTCTTGGTTTGGCTACTTGGAGGTGGAGAAGCTTGCTTCTTTAT
upper sequence: GLYMA09G00460.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv19s0027g01090.t01 (Vitis vinifera), 3'ss of exon 11
atatatcagcagcagcaggtcactcaagtgatttcatttattttctccatctgtctttaggaacttcgtactagttaatattgttttta----ttttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCTGATGGCTCTTGGTATGGATACCGTGAAGTGGAAAAGCTGGCATCACTTT
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----atctatatttctgtggttctttaatatattacttcataaaaaaaaaaaaaatgtggttttactaaaatccctaatatctgtttgaaattttctgttatagAAGTTGTGCAATGAAATGGGGCCTATAGTAACTTTCAACTTGAAACGACCAGATGGTTCTTGGTTTGGATACCGTGAAGTGGAAAAATTGGCTTCTCTATMapped 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|151402728|gb|EV272541.1|EV272541EST: ATGGCAATGGATCTAGTGTCTGCATCCTCTATGGACACCATAATTCAATG AAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCT
genomic: ATGGCAATGGATCTAGTGTCTGCATCCTCTATGGACACCATAATTCAATGgttagtttgt ... tttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCT
EST:
gi|7147103|gb|AW509025.1|AW509025EST: ATGGCAATGGATCTAGTGTCTGCATCCTCTATGGACACCATAATTCAATG AAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCT
genomic: ATGGCAATGGATCTAGTGTCTGCATCCTCTATGGACACCATAATTCAATGgttagtttgt ... tttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccatctgtctttaggaacttcgtactagttaatattgtttttattttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCTGATGGCTCTTGGTATGGATACCGTGAAGTGGAAAAGCTGGCATCACTTT
ttttaat putative branch site (score: 3)
tttttatttt CT-rich tract
tactagttaatattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatatcagcagcagcaggtcactcaagtgatttcatttattttctccatctgtctttaggaacttcgtactagttaatattgtttttattttaatccagAAACTGTGTCATGAAATGGGTCCAATAATTTCATTCAACTTGAAACGGCCTGATGGCTCTTGGTATGGATACCGTGAAGTGGAAAAGCTGGCATCACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG