Sequence
atgc intronic sequence ATGC exonic sequencegtctctgtctatctcttgtatcatcaagaaagccattgttatgttaattcgataggatgttaaaaggaatagtgtgttgtgtctcatagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20420.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
------gtctctgtctatctcttgta--tcatcaagaaagccattgttatgttaattcgat---aggatgttaaaaggaatagtgtgttgtgtctc-atagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
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gaggatggcttgacttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagttta-tctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------------------gtctctgtctatctcttgtat-catcaagaaa--gcc-----attgttatgttaattcgataggatgttaaaaggaatagtgtgttgtgtct-catagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
|| | || ||| | | | |||| ||| | || || || | | || | || | || | || | |||| |||||||| |||| || ||||||| || ||| | ||||||||||||||||||||||||||||| || |||||||||||||| |||||||| || |
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaac-caatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 7
gtctctgtctatctcttgtatcatcaagaaagccattgttatgttaattcgataggatgttaaaaggaatagtgtgttgtgtctcatagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA----------------------------------
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--------------cttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacc-tgt--------acaggtcgctgctgccaaagcagatttgaactatattgGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTATAAAGTTGCATGGTGGTACGCCCGCCAATTTTCT
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------------gtctctgtctatctcttgtat-catcaagaaagccattgttatgttaattcgataggatgttaaaa----ggaatagtgtgttgtgtctcat--------------------agGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
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gttgggttacttcttttaatttcttgaccctgttttatctgtgatgtaagtggaaagtagcacatgtacataccataaaggcaatccccctctcttcacaactacaaggtaaaactaaagaacaatatgtaatgttctatttgtggtttcactgtacaatagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8
gtctctgtctatctcttgtatcatcaagaaagccattgttatgttaattcgataggatgttaaaaggaatagtgtgt-tgtgtctcatagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
||| || | | | | | ||| | | || || | | | | |||| ||||||||| | || |||||||||| || || ||||| |||||||| |||||||||||||| || ||| | || |||||||||||||| ||||
-------------------------------------gtt-tgagaccttgttcata-gtttcacgttttaatgcctgttcgaaaaacagGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgttatgttaattcgataggatgttaaaaggaatagtgtgttgtgtctcatagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
tgttaat putative branch site (score: 3)
tatgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctgtctatctcttgtatcatcaagaaagccattgttatgttaattcgataggatgttaaaaggaatagtgtgttgtgtctcatagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA