Sequence
atgc intronic sequence ATGC exonic sequencegtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51850.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgct--agAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
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---------------------------------------------aaggtcactacttacattaattagtataaataacttgttaacttttgttattttcctttttttcttgggg--aatcttgatatcctttcttttttaccacagAACATCCATGGCTTCAAAATGCTAAGAAAGCTCCAAATGTTCCTCTTGGAGATATTGTGAAGTCAAGGCTCAAACAATTTTCTAGAATGAATAGATTCAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
||| | ||| | | ||| | || || | || ||| | | | | | || | || | ||| || | |||| | | |||||| | ||| |||| || || ||||||||||| |||||||| ||||||||| |||| ||||| ||| |||| || |||||| |||||| |||||||
--------------------------------------atcatgttttaccacgtatttccttttttctttgatcagactc-agacagt--gatatacaggcttggtactcaagatagctgtt----tcacttctgttgtcgcagAGCATACCTGGCTTCAAAATGCTAAGAAAGCTCCAAATGTTCCACTTGGAGATATTGTAAAGTCAAGGCTGAAACAGTTTTCAAGGATGAATAGATTCAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
| || || | | || | | | ||| | | || | |||| ||| || |||| | || ||| | | || |||||||| | | |||||| || ||| |||| || || ||||||||||| ||||||||||||||||| |||| ||||| ||| |||| || |||||| ||||||| |||||||
--------------------------------gttttcatgatgtatagttgtatacatgttcaa--agtcca----tatggaattacct---ggcatcccatttagg---gctcatgcctctttt-ttgtttctgttatcacagAGCATCCCTGGCTTCAAAATGCTAAGAAAGCTCCAAATGTTCCTCTTGGAGACATTGTAAAGTCAAGGCTGAAACAGTTTTCAAGGATGAACAGATTCAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G088361_T01 (Zea mays), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
| |||| || ||||| | | | | ||| | || || | | | | | | | | | | |||||||| | | |||||| || ||| |||| || || ||||||||||| || |||||||||||||| |||| ||||| ||| |||| || |||||| ||||||| |||||||
--------------------------------------------tcgaattacctagcatcccattgccccctcccctctttgggggttcaggtaggtactctaaagtcccccctccccctcttct-ttgtttctgttatctcagAGCATCCCTGGCTTCAAAATGCTAAGAAAGCTCCAAACGTTCCTCTTGGAGACATTGTAAAGTCAAGGCTGAAACAGTTTTCAAGGATGAACAGATTCAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgt-tattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
|| || | || | | || || | |||||||| ||||| | | | | |||| | || || | |||| || || || ||| || | ||| |||| || |||||||| ||||| ||||| |||||||||||| |||| ||||| ||| | || |||||||| |||||| |||||||
--------------ttttcccccaaaagtcatacaactcccacctctgtattatcttttttcactttgtcctttttgattgaggaatgct----gacatttc-------------cccgcaaaaaatac---------------agAACATCATTGGCTTCAAAATGCAAAGAAGGCTCCTAATGTCCCTCTTGGAGATATTGTAAAGTCAAGGCTCAAACAATTTTCTAGGATGAATAGATTCAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 5
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgat-ctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA-
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--------------------------------------------aaaaaaaagatataaacattattgttgtagttatgttgatgacttgtcatagcacatcttgt---tttaattcaaggttcatcttgttttcttgtattccagaGCATCCCTGGATTCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCAATGATGAACAGATTCAAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttt-tgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
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---------------------------------------------aaaaatatatataaacattattgttgtagttatgttgatg-acttgtctgagcacatcttgttttaattcatggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
upper sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 3
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagatttttt-ttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
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---------------------------------------------gattttatgcatgatgtttagtagttgaaatatattaaaattgcatgatggatgccaaattatgttttgttcaatttatactttttctctctgcttgc-agAGCATTCTTGGCTCCAGAATGCTAAAAAAGCTCCAAATGTTCCTCTTGGAGATGTTGTCAAGGCAAGGCTTAAGCAGTTTTCAATGATGAACAGATTCAAMapped 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|86063796|gb|DR359553.1|DR359553EST: AATGTTAGAGCCTGATCCAAAGCGTCGGCTGACTGCAAAGCAAGTGCTTG AGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAG
genomic: AATGTTAGAGCCTGATCCAAAGCGTCGGCTGACTGCAAAGCAAGTGCTTGgtacatagaa ... catttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAG
EST:
gi|116407590|gb|EG450182.1|EG450182EST: AATGTTAGAGCCTGATCCAAAGCGTCGGCTGGCTGCAAAGCAAGTGCTTG AGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAG
genomic: AATGTTAGAGCCTGATCCAAAGCGTCGGCTGACTGCAAAGCAAGTGCTTGgtacatagaa ... catttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
tttctcattt CT-rich tract
attttttttatgctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttttgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA