Sequence
atgc intronic sequence ATGC exonic sequence...gtttttagcattcaatctattgctgtcttgtttcatgattttcaagatgacagctagtggtctctaagatctctaattcatgatacctgtggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGACAAGCCAATTATAGTGCTGCAAAAGCAGGAGTAATTGGCCTGACAAAAA
Basic information
species | Glycine max |
transcript | GLYMA18G01280.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 7
gtttttagcattcaatctattgctgtcttgtttcatgattttcaagatgacagctagtggtctctaagatctctaattca--tgatacctgtggttt--tgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGACAAGCCAATTATAGTGCTGCAAAAGCAGGAGTAATTGGCCTGACAAAAA
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-ttttgtggtctgaatttaa-gaagttttgttaaaaagagcttctattcatatccat--gtcaccatgagtactgatttgcttgttttttgtgttgaaatgcagGGAAAAATCATCAACATAGCATCAGTTGTTGGTCTTGTTGGTAATATTGGCCAAGCTAATTACAGTGCTGCCAAGGCTGGGGTTATTGGTTTGACGAAAA
upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g01840.t01 (Vitis vinifera), 3'ss of exon 7
gtttttagcattcaatctattgctgtcttgtttcatgattttcaagatgacagctagtggtctctaagatctctaattcatgatacctgtg-gttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGACAAGCCAATTATAGTGCTGCAAAAGCAGGAGTAATTGGCCTGACAAAAA
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acttctgaatttcataattgtgctgtcct-tttcttttcttttcttttttttccaatttccctattgcttctatatgtcctcatttttctctgttgttcagGGAAGAATTATCAACATATCCTCTGTTGTTGGCCTGGTTGGCAATGTTGGACAAGCCAATTACAGTGCTGCAAAGGCAGGGGTAATTGGCTTAACAAAAA
upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0010g02670.t01 (Vitis vinifera), 3'ss of exon 7
gtttttagcattcaatct---attgctgtcttgtttcatgattttcaagatgacagctagtggtctctaagatc-tctaattcatgatacctgtggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGACAAGCCAATTATAGTGCTGCAAAAGCAGGAGTAATTGGCCTGACAAAAA
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-ttatttaaatacacttggagagggagattttgatttatg-tggatattttgatatcttttctctaatccaatcctctggct--tggtcctgccgaattcacagGGAAGGATAATTAATATAGCATCAGTTGTTGGTCTGGTTGGCAATGTTGGGCAAGCTAATTACAGTGCTGCGAAGGCAGGAGTAATTGGCCTTACAAAGAMapped 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|58017082|gb|CX703824.1|CX703824EST: GCTGCTGCTAAGATTATGATGAAGAAAAAGAAG GGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGA
genomic: GCTGCTGCTAAGATTATGATGAAGAAAAAGAAGgtgacatacc ... ggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGA
EST:
gi|192333775|gb|FK025498.1|FK025498EST: GCTGCTGCTAAGATTATGATGAAGAAAAAGAAG GGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGA
genomic: GCTGCTGCTAAGATTATGATGAAGAAAAAGAAGgtgacatacc ... ggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGA
EST:
gi|192334677|gb|FK025224.1|FK025224EST: AAGATTATGATGAAGAAAAAGAAG GGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGA
genomic: AAGATTATGATGAAGAAAAAGAAGgtgacatacc ... ggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgacagctagtggtctctaagatctctaattcatgatacctgtggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGACAAGCCAATTATAGTGCTGCAAAAGCAGGAGTAATTGGCCTGACAAAAA
ctctaat putative branch site (score: 3)
taattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttagcattcaatctattgctgtcttgtttcatgattttcaagatgacagctagtggtctctaagatctctaattcatgatacctgtggttttgcagGGAAGGATCGTCAATATTGCATCAGTTGTTGGTTTGGTTGGCAATGTTGGACAAGCCAATTATAGTGCTGCAAAAGCAGGAGTAATTGGCCTGACAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - -gcattca
- - - - - - - - - - tgctgtc
- - - - - - - - - - - - - - - -ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - gctagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatacc