Sequence
atgc intronic sequence ATGC exonic sequencegttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42020.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 3
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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-----gttagtaatgacaagacattcatgtgcttagttaactcaagcggtgatt-------ctgtggaagccattgctcactt--ctgctctttca-tgttttcagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 3
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
||| ||| | ||||| | || | | || || |||| | | ||| | | || || || ||||| | | ||||| |||||||||||||| || ||||| || ||||||||||| ||||| ||||| || |||||||||||||| |||||||| || || ||||||||||||||
--------gttagtaactgaaccattctgctggttacctctagtag--------ttgttatgtaaaaatgtggtggcttacttcctta-tgttttgttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 3
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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--------gttagtaactgaacaattctgctggttacctctagtag--------ttgttatgtaaaaacgtggcggctcacttccttgtgttgtgtttttttgcagCGTACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 3
------gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgt-ttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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gtaactggaagtctggaac-aattcacgactt--atttcaactgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAATGAACCCACTGCTGCTGCCAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
------gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgatt-gattgtttat-ttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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gtaactggaagtctgaaac-aatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaa-atgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
------gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttct-tatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
| ||| || || || | || | | | | || | | || || | || || || ||| | | | | || || |||||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||| ||||||||||||||||| || || ||||||||||||||||| ||
gtaactggaagtctggaac-aactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatg-ccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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----------------------gtaactggaa-gtctggaaca-attcatgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 3
------------------gttagtttgt-tgttaattcgggttttctgttatatatgtagtggagagataaatt----tcttatctgtattggtgattgattgtttatttggtgtttg-actatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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gtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttcttgaaatgtgaattagcattttgttcattaggatgttttact-catattagctttccatgcaacccgcagCTTACTTCAATGATGCCCAGAGGCAGGCTACAAAGGATGCTGGCGTTATTGCTGGCCTGAATGTTGCACGAATTATTAATGAGCCAACTGCTGCAGCTAT
upper sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
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------------gtaatgtaaa---acagtttgatttgatg-gatgaagtaaattgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164111746|gb|EL976160.1|EL976160EST: CGAAGCTTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAG CTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGC
genomic: CGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtttgt ... ctatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGC
EST:
gi|125185127|gb|EL200081.1|EL200081EST: TCACTGTTCCAG CTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTG
genomic: TCACTGTTCCAGgttagtttgt ... ctatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTG
EST:
gi|47829411|gb|CK119095.1|CK119095EST: CGAAGCCTACCTTGGNNNNNNNNTCAAGGACGCTGTTGTCACTGTTCCAG CTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTGATTG
genomic: CGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtttgt ... ctatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
gtttgac putative branch site (score: 4)
attgattgtttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT