Sequence
atgc intronic sequence ATGC exonic sequencegtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgataattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18100.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 5
gtaaataaaaagtagaatcagttttagat--tcctttaagaaataaaatgaatcaaagtgatgataattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
| |||||||| | | ||| | | | |||||| | | | ||| | | | | || ||| || ||| || | |||||||||||||||| |||||||| | || |||||||| ||| ||| || |||| |||||||||||||||||| | |||||||| ||||| |||||
-------------tcattcagttttgttttgttttttgtgtgtgtgtgttgctgttggtgatgctccatttttagatgatgaagatattttatgtatcactttgtttt----actagCTGCTGGAGCTGGACTCACTGGAAGCAAAATGGCTAGAAGAGTTGGGGATGTTGAGGAGTTTGAATTCAAAGCTGTAGGAGAAAACCATAACCAAGGT
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 5
gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgat---aattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
| | || | || || || | || | | || | | | | |||| | || || | | |||||| |||| | || ||||||||||||||| || ||||| | || |||||||||||| ||| | |||| |||||||||||||| ||||| |||||||| ||||| |||||
----------attgtgataaaagttgcatctgttggacaattgactccttgcatattccttttttaaattaagaaattttttatgtatctctttgtt-ctacttttgcc-------agCTGCTGGAGCTGGACTTACTGGAAGCAAAATGGCTAGGAGAGTTGGGGGTGTTGATGAGTTTGAATTCAAGGCTATAGGAGAAAACCATAACCAAGGC
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 5
gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgataattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
| | | | | | || || || ||| | || | || | | ||| | | || || || | |||||| |||| | || ||||||||||||||| || ||||| | || |||||||||||| ||| | |||| |||||||||||||| ||||| |||||||| ||||| |||||
---ccttgatcttgcagttatttctacttttttttta----tatcagttattttccttttttaaatgatgaattttttcgtgtatctctttgtt-ctacttctgcc-------agCTGCTGGAGCTGGACTTACTGGAAGCAAAATGGCTAGGAGAGTTGGGGGTGTTGATGAGTTTGAATTCAAGGCTATAGGAGAAAACCATAACCAAGGC
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G17160.1 (Glycine max), 3'ss of exon 3
----------------------------------gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgataattgtatagttctt--agtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAA--CTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
|| || | | | || | | ||| | | || ||| || | || | || | | | | || ||| | | | | | | || ||||||||||||||| | ||||| | || |||||||||||| | | | |||| |||||||||||||| ||||| |||||||| ||||| |||||
gttcttatctgttattgtgataaaagttgcatctgttggacaattgccttcttgatcttgcagttatttctacttttttttttatatcagttattttccttttttaaatgatgaaattttttgtgtatctctttgttctacttctgc-cagctgctggagctggatttactggaagcaaaatggctagGAGAGAGTTAGGGGTGTTGATGAGTTTGAATTCAAGGCTATAGGAGAAAACCATAACCAAGGC
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 4
gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaa--agtgatgataattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
| ||||||| || | | | || || |||||| | || | ||| | | || ||| || ||| || | |||||||||||||||| |||| ||| | || |||||||||||| ||| || |||| ||||||||| |||||||| | || |||| ||||| |||||
------------ttcttgcagtttttt-tttttgtgtgtgtgtgtgtgtttctgttggtgatgctccttttttagacgatgaaaatactttatgtatcactttgtttt----actagCTGCTGGAGCTGGACTCAGTGGAAGCAAAATGGCTAGGAGAGTTGGGGATGTTGACGAGTTTGAACTCAAAGCTGTAGGCAAAAACCATAACCAAGGT
upper sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgataattgtatagttcttagtcttctgttttgtttctac--atgtgttcatgaat--agCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
| ||| | | | | | | | | | | | | ||| ||| ||||||| || ||||| || ||||||||| ||||| ||||| |||| || |||||||| |||||||| | || || ||||| |||||||||||||||||||| ||||| |||||
----------------------------------------gtgaaacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgataattgtatagttcttagtcttctgttttgtttctacatgtgttcatgaatagCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA