Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaagcaaaatgtacataccctcggcttctcaatatgtcttaactggtatgttatttgatgtggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G64550.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaa-gcaaaatgtacataccctcggcttctcaatat--gtct-----taactggtatgttatttgatgtg-gcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
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--------------------------------------------------gtaagttcaagcatcatttttatctttcct---ttacatccagcaacaattgctaggttgcacca-tgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG
upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 13
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaagcaaaatgtacataccctcggcttctcaatatgtcttaactggtatgttatttgatgtggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
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---------------------------------------------------------------------------------------------tgggatgctaggctgtaaacacggtgttttttaaaacttgtttagtacc-tgtgcttgcaattatgttatttaaattttcctatt----cgttattt--ttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG
upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 13
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaagcaaaatgtacataccctcggcttctcaatatgtcttaactggtatgttatttgatgtggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
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-------------------------------------------------------------------------------------------gacaaggtgacaatttacttatgt-ttggagaaacaggaggaggggggtacctgtgcttgcaactatgttattaaattttcctatttgaaattttct--------gcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCGCTGCAGCCAATGTATACTTTGTCAG
upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 14
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaagcaaaatgtacataccctcggcttctca-atatgtct-taactggtatgttatttgatg-tggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
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---------------------------------------------------------------------------------------------------tctccattttttgtgggttat---cctcttctatttttggaatatcttt-tgcccgaatgttatcacatgagtgaatcactgatgtgaaattggcttcttgcagGGGGTGCCAGAACAGAAGCTCCGAGCTCATTTAGGTTCATTTGGTGTAACAGGAAATCTTGCTCTTCAGCCCATGTACACTTTATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacataccctcggcttctcaatatgtcttaactggtatgttatttgatgtggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
tatgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaagcaaaatgtacataccctcggcttctcaatatgtcttaactggtatgttatttgatgtggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG