Sequence
atgc intronic sequence ATGC exonic sequencegtatgttatgttacagctaggcttattagcaagaaggatttccaaatttcaggaatgtcatggctgtttctttctttgatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72960.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 9
----------gtatgttatgttacagctaggcttattagcaagaa-ggatttccaaatttcag--gaatgtcatggc---tgtttctttct-----ttgatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
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gtaagttcttcattcctttgatattgctaatcttactgatgttcttgtatagcaagattttatatgaagtttatagtaaatgtttattcttggtaacaaatgaccagGTTGAAGTTGTTGCTCTTTCTAGTTATGAAGAAAAGGAAGAGCAGTTTAAAGAGCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 9
----------gtatgttatgttacagctaggcttattagcaagaaggatttccaa------atttcaggaatgtcatggctgtttctttct-----ttgatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
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gtaagttcttcattcctttgatattgctaatcttactgatgttcttgtttagcaagattttatatgaagtttatagtaattgtttattcttggtaataaatggccagGTTGAAGTTGTTGCTCTTTCTAGTTATGAAGAAAAGGAAGAGCAATTTAAAGATCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 9
------gtatgttatgttacagctaggcttattagcaagaaggat-ttccaaatttcaggaatgtcatggctgtttctttctttg---atggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
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gtaatcacttaacttattaatgttca-cttacacataatagagttgtattggacttttatagtactaattctttgcacttggctacaaatgaccagGTTGAAGTTGTTGCTCTTTCTAGTTTCGAAGAAAAGGAAGAACAATTTAAGGAGCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 10
-----------gtatgttatgttacagctaggcttattagca-----agaaggatttccaaatttca--ggaatgtcatggctgtttctttcttt--------gatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
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gtaagatcatcattcctttttgaatcacttaacttaataatgttcacttaaacatagtagagttatattggacttttataataattttttgcacttggctacaaatgaccagGTTGAAGTTGTTGCTCTTTCTAGTTTCGAAGAAAAGGAAGAACAATTTAAGGAGCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------gtatgttatgttacagctaggcttattagcaagaaggatttccaaatttcaggaatgtcatggctgtt-tctttctttgatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
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gtaagatgttacaattttaggcaagataagcttaggaatgtccatttctatttttcacgaggatttgctt-ttggatttatgtttggcttactatatctattaaatggtcagGTTCAAGTTACAGCTCTTTCTAGTTATGAGGAGAAGGAAGAACTGTTTAAAGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaggatttccaaatttcaggaatgtcatggctgtttctttctttgatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
ctttgat putative branch site (score: 5)
ctgtttctttcttt CT-rich tract
aaatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttatgttacagctaggcttattagcaagaaggatttccaaatttcaggaatgtcatggctgtttctttctttgatggttagGTTGAAGTTGTTGCTCTTTCCAGTTATGAGGAGAAGGAAGAACAGTTTAAAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG