Sequence
atgc intronic sequence ATGC exonic sequencegttttaatatagtggttacaacatttttttgaatatatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G18050.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 10
--------gttttaatatagtggttacaa-catttttttgaatatatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggtt-tagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
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cacgatatatttgtgcattctctttcctttcatccttatggatgtgacagtcatttttaaagttgtttgttttccatttatgtttgatatgtgactgtagATCATGTATGAAGAAGCAAGCCAAGTTGCAACTGATGCAGTTGGTAGCATCAGAACAGTAGCATCTTATTGTGCTGAGAAGAAAGTGATGACAAAATACA
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g50160.1 (Oryza sativa), 3'ss of exon 9
---------gtttta----atatagtg-gttacaacattt-ttttgaatatatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
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agtttctaaatttcatgacgaataatgagaaacaacattcactctagatacatttttcacaacttgc---ttaaattgtgacaatgaattcctggtttggc--agATGTTGTATGAAGATGCAAGTCAAGTGGCTACTGATGCAGTAAGCAGCATCAGGACTGTAGCTTCCTTTTGTTCTGAGAAAAGAGTGATGACAATGTATG
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 9
gttttaatatagtggttacaacatttttttgaatatatcccggtttagtcgcg-atttcgggtttactgatcg-attttttttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
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--gttagcct--tacttgcaac--tttgtcaattccatt--aatgaaattatgcattatggacatcatgagaatattttgtctgctgtgtagGCAAAGTATGAAGAGGCAAGTCAAGTGGCAAATGATGCTGTTGGTAGCATCAGAACCATTGCATCATTCTGTGCCGAATCAAAGGTGATGGATATGTACA
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 9
gttttaatatagtggttacaacatt---tttttgaatatatcccggttt-agtcgcgatttcgggtttactgatcgatttttt--ttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
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----------gttggtaacactcctcacttcccggttatttcatcatttgaaatgaattcttagattcactaaggcccttcaaaacttcatgttagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTGGCAGCATCAGAACTGTTGCATCATTTTGTGCGGAAAAGAAGGTGATGGATATGTATC
upper sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 11
gttttaatatagtggttacaacatttttttgaatatatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggttt-----agGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
|| || | | | |||| | | | ||| | || || ||| | | || || | || ||| ||| ||||||||||||||| |||||||| || ||||||||||| |||||||| |||||||||||||| || ||||| ||| |||| |||||||| | || |
----------gtcagtagcattccctgtgagtatatgttctgcatta--tgaaatgacgtgttgattcattgaagatattataaattttttgtagGTGATGTATGAAGAAGCAAGTCAAGTTGCAAATGATGCAGTTAGCAGCATCAGAACGGTTGCATCATTTTGTGCTGAGAAGAAGGTGATGGAGATGTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
tactgat putative branch site (score: 2)
ttttttttctggttt putative PPT
attttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttaatatagtggttacaacatttttttgaatatatcccggtttagtcgcgatttcgggtttactgatcgattttttttctggtttagGCGATGTATGAAGAAGCGAGTCAAGTGGCGAATGATGCAGTGAGCAGCATAAGAACGGTTGCATCTTTCTGTGCAGAGGAGAAAGTGATGGATTTATACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA