Sequence
atgc intronic sequence ATGC exonic sequenceTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttgttgactagcaaatatcttgttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78920.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 12
TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttgttgactagcaa-atatcttgttgcag
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ATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAGGTCAGGAGACAGTTTATTGAGAGGCCTGGCATTATGgtgagtacatgcatataattaagtttgtcat-ttttcttatgcctataaaagt--taatgctaacttctaatataatgttatgcag
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 4
TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttgttgactagcaaatatcttgttgcag
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ATTCCTGTTCAGTGCATGGGCTTGCTCAGCAGTTGGCAAAACTGCACAGGAAGTTGTTAAAGAGGTCAGGAGACAATTTATTGAGAGGCCTGGTATCATGgtgagtacatgattaccatgaagttcttcag---tccttttatgcttggaaaagcagatgctaacatgtaacaatatcatc-cag
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 12
TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcacctttt--cttgtgtattggcttgtaccgttgttgactagcaaatatcttgttgcag
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ATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGGTATAATGgtgagtttgggtttgtaaagtaatattatgtatgccagtttaggttttgatcttctctctttttttcccttttatgcttt-tgacag
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G24120.1 (Glycine max), 5'ss of exon 11
TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttgttgactagcaaatatcttgttgcag
|| | |||||||||||||| || | || ||||| ||||||||||||| ||||| |||||||| |||||||| || |||||||||||||| ||||||||||| | ||| | | | | | | ||| || | || || | | ||| || | |||
ATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGGTATAATGgtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttt-tgacag
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G24120.2 (Glycine max), 5'ss of exon 12
--------TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttgttgactagcaaatatcttgttgcag
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ATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTGCACAAGAAGTTGTTAACGAAGTGAGAAGGCAGTTCATTGAGAGGCCTGgtataatggtgagtttgggtttgtaaagtaatattatgtatgacagtttcgattttgatgaccgctttttttcctgtttatacttt-tgacag
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 12
TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttg-ttgactagcaaatatcttgttgcag-----------
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TTTCCTATTTAGTGCATGGGCATGTTCTGCAGTTGGCCGGACTGCTCAAGAGGTTGTCAATGAAGTAAGAAGACAGTTTATTGAGAGGCCAGGTATCATGgtgagtatgattctctatagcatttttatggtttatcatgaatgtaggttttaatttttaattgatgcatgaaattgttttaacatgtttgctacagMapped 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|116443900|gb|EG486492.1|EG486492EST: AGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATG GAGTACAAGGAGAAGCCAGATTATAGTCGCTGTGTCGCCATAGTCGCATCT
genomic: AGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatat ... cttgttgcagGAGTACAAGGAGAAGCCAGATTATAGTCGCTGTGTCGCCATAGTCGCATCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTGCACAAGAGGTTGTCAACGAAGTAAGAAGGCAATTTATTGAGAGGCCTGGCATAATGgtgagcatatttttccttttgagtgcttcaccttttcttgtgtattggcttgtaccgttgttgactagcaaatatcttgttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG