Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttaaccgcaactctattttgacgcgaaaaatttgtttcgatttgagatttaatgtggattgaaaacatatcagGCGGGTAAAAGGAGGGCAGAGAAAAGGCACAAGTTCATGGAAGAGTATCTTAAGGAGTTCTATGAAGAGTGGGATGGGTCAACTTGAAAAGTTAAAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17330.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g34470.1 (Oryza sativa), 3'ss of exon 6
-----------------gtaagtttaac---cgcaactctattttgacgcgaaaaatttgtttcgatttgagatttaatgtggattgaaaacatat-cagGCGGGTAAAAGGAGGGCAGAGAAAAGGCACAAGTTCATGGAAGAGTATCTTAAGGAGTTCTATGAAGAGTGGGATGGGTCAACTTGAAAAGTTAAAAATG
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atcttaataccatgtactccaatttacctagtacaaacattccttgtagaatcccattatctcttcctttggcgttgacaccatttcactttgtgcatagGCCGGGAAAAAGAGAGCAGAGAAAAGGCACAAGTTCATGGAGGACTTTGTGGCTGAATTCTATGAAGAGTGGAGTGGCAGAGCTTGAAGTTGACCAACCA
upper sequence: AT1G17330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G02920.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------gtaagtttaaccgcaactctattttgacgcgaaaaatttgtttcgatttgagatttaatgtgga--ttgaa----aac-----atatcagGCGGGTAAAAGGAGGGCAGAGAAAAGGCACAAGTTCATGGAAGAGTATCTTAAGGAGTTCTATGAAGAGTGGGATGGGTCAACTTGAAAAGTTAAAAATG
|| ||| | | | || | ||| || || | | | | || | |||| ||||| ||| || |||||| || |||||||||||||||| |||||| ||||||||||| |||| | | || |||||||| || || ||| |||| | || | | || |
gtaggctatattactatttggctgaaatgatcaaattttgacgaagaccaaagtgtgcatttttttttg-ttaaagtctgtcaagaagtatatgcctgtgtattaaatctgtcatggaatttgaatctcaactacctatttcagGCTGGGAAAAGGAGGGCAGAGAGAAGGCATAAGTTCATGGAGGAGTTTGTGAAAGAGTTCTACGACGAATGGAATGGTTTAAGCTAATAAACCATTCCAC
upper sequence: AT1G17330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g02070.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------gtaagtttaa--ccgca-actctattttgacgcgaaaaatttgtttcg-------atttgagatttaatgtgg----attgaaaacata---tcagGCGGGTAAAAGGAGGGCAGAGAAAAGGCACAAGTTCATGGAAGAGTATCTTAAGGAGTTCTATGAAGAGTGGGATGGGTCAACTTGAAAAGTTAAAAATG
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gtaaatacctgaagcctgaaacggaccattatcagcttttggcacatgcattcatgcaaatttgttggtgcagtgactttgtgcctgcataatacatgtttataagagatggctcttttatttatttatttataattttttttggttatatctggtgtttgagttcagGCTGGGCAGAGGAGAGCAGAGAAAAGGCACAATTTCATGGAGGAATTCTTGAAGGAGTTTTATGAAGAGTGGGATGGAAGAGCTTGAATAAG-------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacgcgaaaaatttgtttcgatttgagatttaatgtggattgaaaacatatcagGCGGGTAAAAGGAGGGCAGAGAAAAGGCACAAGTTCATGGAAGAGTATCTTAAGGAGTTCTATGAAGAGTGGGATGGGTCAACTTGAAAAGTTAAAAATG
atttgagatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttaaccgcaactctattttgacgcgaaaaatttgtttcgatttgagatttaatgtggattgaaaacatatcagGCGGGTAAAAGGAGGGCAGAGAAAAGGCACAAGTTCATGGAAGAGTATCTTAAGGAGTTCTATGAAGAGTGGGATGGGTCAACTTGAAAAGTTAAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA