Sequence
atgc intronic sequence ATGC exonic sequence...attaaacctaattatttcttattttgtattatgctttcactcatacatattagtagatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
Basic information
species | Glycine max |
transcript | GLYMA18G36660.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G36660.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 16
attaaacctaattatttcttattttgtattatgctttcactcatacatattagtagatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
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--------------gtttttctatagctctgagatggtgaacaaagtgtcttctatgcttaaactaatttaaatgccccggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
upper sequence: GLYMA18G36660.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G24870.1 (Arabidopsis thaliana), 3'ss of exon 17
attaaacctaattatttcttattttgtattatgctttcactcatacatattagtagatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
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--------------gtttttctatagctctgagatggtgaacaaagtgtcttctatgcttagactaattaaatg-ccctggatatgtctgtgatattcagGGAAGTGCGAGACAGTTGTTTCAACGACTGCAAGGGCCAATGGAGGAAGATACCCTGAAGTCTCATTTTGAGAAGATTTGTTTGATTGGGAAGAAATTAC
upper sequence: GLYMA18G36660.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv07s0005g06680.t01 (Vitis vinifera), 3'ss of exon 17
------------------------------attaaacctaatta-tttcttattttgtattat--gctttcactcataca-tattagta-------gatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
||| | || || ||| ||||||| | ||| | ||| || | | || | || | ||||||| | | | ||| | | ||| ||||| |||||||||||||||||||||| |||||| || || ||| ||||| || || |||||||| ||||| ||||| || |||||||||| |||| |
gtaagaattttgattttccctttttgacaagttagaaatagttccttttttatttttttgtattgatgtaaacttgtagactgttgacattgagctaattttagctgtttgaatttatctctgtttctaca-cttgctcagGGCAGTGCCAGACAGTTGTTTCAACATTTGCAGGGGCCGATGCTAGAGGAAACCCTCAAGTCTCACTTTGAGAAAATCATTTTGATTGGGCAGCAGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattagtagatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
gtttgat putative branch site (score: 5)
tatcttt putative PPT
ttttaaatttttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaaacctaattatttcttattttgtattatgctttcactcatacatattagtagatcctcattgtttgattggttttaaatttttgtatctttagcagGGTAGTGCCAGACAGTTGTTTCAACGTTTGCAAGGACCAATGGAGGAGGATACTCTGAAGTCTCATTTTGATAAAATTATCAAGATTGGGCAGAAGCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - -tatgctt
- - - - - - - - - - - - - - - - - - tcactca