Sequence
atgc intronic sequence ATGC exonic sequencegtaatgatcaatccctagtaattgttgcaagaataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
gtaatgat-caatccctagtaattgttgcaagaataagtgctttaaacttacaag-gcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
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gtagtttcgtcttcctttttaatcaagtgcaaagtgtgataattgttctaacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC
upper sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g49810.1 (Oryza sativa), 3'ss of exon 7
-------------------------gtaatgatcaatccctagtaattgttgcaagaataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
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gtaagtgcaatctagagttcaatttggaattgcaatttcttggcaatgactg-agaaacatgtattcggtaaaaactgctcatttt---tctaccatgcagGAGCCTGAGAAACATGTATTCCATCTTGTTACTGACAAGCTGAACTTTGGAGCAATGAACATGTGGTTTTTGTTGAATCCACCTGGAGATGCGACAATCC
upper sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
------------gtaatgatcaatccc-tagtaattgttgcaag-aataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
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gtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgataagtgttctga--caactatgtatggcataacctttt--cagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
upper sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
gtaatgatcaatccctagtaattg-ttgcaagaataagtgctttaaa-------cttacaa-ggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
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gtattttccatgcacttttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
upper sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 7
-----------gtaatgatcaatccctagtaattgttgcaagaataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
||| | | || | | | | | ||||| ||| | | | | | || | ||| ||||| || | ||||||||||| ||||||||||| ||| | ||||||||||| |||| |||||||||||| ||||||| ||||| | || |||||||
gtattttgcgtgtacttttagtcaattattcaattgcactccactaagtagtttctaatggtgatgtttggcatgtcttttt--cagGAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCCACCATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgcaagaataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
aacttac putative branch site (score: 2)
tttattt putative PPT
tttaaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgatcaatccctagtaattgttgcaagaataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC