Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14450.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 3
gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
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------------------------------------------------------------acaatat--caagtactg--caatttctggg-----gttattgtttttattactgaaat-----tatggaatgaaaatt-----tccaaaaccatactaataccctct-ctctcctgaagGTCGTTGACTGCAGAATCTGTGGTGATCCACACTCAGTTCTAAGGTTTGCATTCATTGAGTTTGCTGATGAAG
upper sequence: AT3G14450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G069816_T01 (Zea mays), 3'ss of exon 3
gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
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-----------------------------------------------------------------------ctgtcaacatgatcttctattatat-caacatgatcttct---attctgtcaacatgatca-atgatgttttttcctaaatcctaatgaacttcctctctctt----agGTTGTTGATTGCAGAATTTGTGGTGATCCCCACTCAGTTCTTAGGTTTGCATTTATTGAGTTCTCTGATGAAG
upper sequence: AT3G14450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18810.1 (Glycine max), 3'ss of exon 3
gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
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------------------------------------------------------------------------ctctagctgaatatctaggatt----taaa---tttgtaagataagtctttcattatgactattaccctacttaggtagtaatgatatttactgatttgaat-tgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCAGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
upper sequence: AT3G14450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40060.1 (Glycine max), 3'ss of exon 3
gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
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------------------------------------------------------------------ggctgaatat---ctaggatttaaatttgaaagataaatcttttgttatgattattaccctacttaggcagt-----------aatgatatttattgtgtcatttgaattgaagGTAATTGATTGCCGAATTTGTGGTGATCCACATTCTGTTCTCCGTTTTGCTTTTGTTGAGTTTGCAGATGAGT
upper sequence: AT3G14450.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0176g00140.t01 (Vitis vinifera), 3'ss of exon 3
gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
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----------------------------------------------tagataggttttacacaaaa--ttgagttttaacttgatagttggtttgt--------tgtggttgatgagactatactttc---------ttaagtttctggaatg-------------cttattttg--aagGTTGTTGATTGTCGAGTTTGTGGTGATCCGCATTCAGTTCTTCGTTTTGCATTTGTGGAGTTTGCTGATGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
aagtaac putative branch site (score: 2)
ttcttcttcttttgt putative PPT
tatagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgatccttaaaatctttaaatgttggttatatctttctatttcatgtgttttggacaatgtgttaaatttagactagtttttgagtccgtgccaaaggttctgttgaaaaaatgttactttggtggtatagttgtgtgtgtgaagtaacgttaagttcttcttcttttgtgaagGTTGTTGACTGTAGAATTTGTGGCGATCCACATTCGGTTCTTCGATTTGCGTTTGTTGAGTTTGCTGATGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT