Sequence
atgc intronic sequence ATGC exonic sequence...ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 2
ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttga--ttgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
||| || | || | | || | | | | | | | || | || | | | |||| | | || | |||| ||| |||| || | | || ||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| | || || |||
--gtttactgcacattttgccctttattactaca-ataatgcctctatatc--atgttac-tagcagctttctttaacgtgtccatccttttgatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 2
--------ttattttcttgt-tgctcagcagtattttgccaagtgtggt----ataattggtttcaactttgcgtaaga----------cataccactaacttttggattcacttgat-tgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
||| | || || | ||| | | |||| | | | | || ||| | || || | | ||| || | |||| || | | | || |||| || | | ||||| || |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||| | || || |||
gtttggacttactcactagtgtcttcataattcttttaatatttctcatctccattgttgacattaagttgaattggaatgaaaaggttcatgcccttcgtttttattttaccctattctgtagTTGGTATTGCTTGGAGATTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGCTTTGTCCGTGGTCAGTTTGACCCCACTTCAAAG
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 3
ttattttcttgttgc-tcagcagta-ttttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttg-attgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
||| || | | | | ||| | || | | ||| || | | || | | ||| | | |||| | || || |||| || | | |||||||| |||||||| |||||||| ||||| ||||| ||||| |||||||||||||| |||| || |||
-tatgttagggcatcattaatagtggctgtgatttatctagtaaaacctgaat--acctgattaacgacttttgttaatgttttcaaccttctcatgttatagTTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
ttattttc-----ttgttgctcagcagt-attttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
||| | | || || | | | || || ||||| | | | ||| ||| |||| | || | ||||| |||| || || ||| | ||||| ||||| || ||||||||||||||||| |||||||| || |||||||| |||||||||||||| | |||||||||
ttaatcacaacagtttctgtttatctgttatactgcca----ttattttcttg-tttagcctttaaaggaaac-cataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
--ttattttct-----tgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
||| | | | |||| | |||| ||||| | | | ||| || ||| ||| | | | |||||| || |||||| | ||| | ||||| ||||| || ||||||||||| ||||| |||||||| || |||||||| |||||||||||||| | |||||||||
aattaatcacaacaaattctgcttgtctgtatactgcca----ttattttcttg--tttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaa-acagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
upper sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
------ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
| | || | | | | | | | ||| | | | |||| | | ||| || || || | ||| ||||| | ||| | || || || ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||||||| ||||||| |||
ctgcaagaaatatcattatagaaattaattgatgggcaaatatag---gattgaataagaaccc---taaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAGMapped 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|164230211|gb|ES103894.1|ES103894EST: TGCCAAAAATCTACGTGTGAAG TTAGCTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
genomic: TGCCAAAAATCTACGTGTGAAGgttttttttt ... ttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
EST:
gi|19875441|gb|AU236272.1|AU236272EST: GCAATTCAGAGAATGCTGTTCCAGCTGATGCCAAAAATCTACGTGTGAAG TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
genomic: GCAATTCAGAGAATGCTGTTCCAGCTGATGCCAAAAATCTACGTGTGAAGgttttttttt ... ttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
ttcactt CT-rich tract
taactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG
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