Sequence
atgc intronic sequence ATGC exonic sequencegttaggccttggtgaaatagattcacaaatacaaaatccgaggcagatcctaaccttgttaataatgtctatgttttcagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 2
gttaggcc----ttggtgaaatagattcacaaatacaaaatccgaggcagatcctaacc------ttgttaataatgtc----tatgtt-------------ttcagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
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gttaggccaggtttggcttaataatctaagaaataaaagatactctttggtttcttttcaattggctgtatgtgatgtctccatatattatatgcctcctactgcagGTTAAATGTTACATACATCAACTGCTATCAGGACTTGAGCACTGTCATAGTCGAAACGTACTTCACCGTGATATTAAAGGATCAAACCTTCTTATTGACA
upper sequence: AT3G05050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 2
gttaggcc----ttggtgaaatagattcacaaatacaaaatccg-----------------------aggcagatcctaaccttgttaataatgtctatgtttt----cagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
|||||||| ||| |||| | | ||||| || || | | || || | | |||| | | | | | | ||||||||||| || ||| | ||||| || ||||| || ||||| || |||| | | | || |||||||||||||||||||||||||||||||| ||
gttaggccaggtttgccttaataatctaagaaataaaatatatgcaccctttggtttattttcaattggccatatttgatgtctccgaatactatgtgtctcctactgcagGTTAAATGTTACATGCATCAACTGCTATCAGGACTTGAGCACTGTCATAGTCAAAACATACTTCACCGTGATATTAAAGGATCAAACCTTCTTATTGACA
upper sequence: AT3G05050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 2
----------------gttaggcct--tggtgaaatagattcacaaatacaaaatcc-------gaggcagatcctaaccttgttaataatgt-ctatgttttcagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
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gttagatcaggtttgccttaaaattacttgtatcatttggtaattggtacattttcttttcaaggagtaggatttgatgtcccctaatactgtgccttcattgcagGTTAAATGTTACATGCATCAGCTGTTATCAGGACTTGAGCACTGTCATAACCGTCATGTACTTCACCGTGATATTAAAGGATCAAATCTTCTTATTGACA
upper sequence: AT3G05050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 2
----------------gttaggccttggtgaaata------gattcacaaatacaaaatccgaggcagatcctaaccttgttaataatgtctatgttttcagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
||| | || | | ||| | || | |||| ||| | | |||| ||||| || ||||| ||||| || ||| | || || || ||||| || ||||| || |||||||| | || || ||||||||||||||||||||||| |||||||| ||
gttagatcaggtttgccttaaaattacttgtatcatttggtaattggtacattttcttttcgagtaggatttgatgtctccaaatactgtcttcattg-cagGTAAAATGTTACATGCATCAGCTGCTATCAGGACTTGAGCACTGTCATAACCGTCGTGTACTTCACCGTGATATTAAAGGATCAAATCTTCTTATTGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatacaaaatccgaggcagatcctaaccttgttaataatgtctatgttttcagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
tgttttc CT-rich tract
ttaataatgtctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggccttggtgaaatagattcacaaatacaaaatccgaggcagatcctaaccttgttaataatgtctatgttttcagGTTAAATGCTATATGAAGCAACTACTTTCAGGGCTCGAGCATTGCCATAACCGAGGAGTTCTACACCGTGATATTAAAGGATCAAACCTTCTTATAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG