Sequence
atgc intronic sequence ATGC exonic sequence...agaaaagtaataacatatattcgagggtagcctgctttcgagactggtgaagacttttgtaatggtcatgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 3'ss of exon 3
agaaaagtaataacatatattcgagggtagcctgctttcgagactggtgaagacttttgtaatggtcat-gactcatgattgg---agttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
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----gaatcacaatgtccatggtctgttcatctttttcttcgatggtcttctcgtactgtagtttctgtcgtcttgcaatttgataaatcctagatgcttccagGTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAG
upper sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G026884_T01 (Zea mays), 3'ss of exon 2
-agaaaagt--aataacatatattcgagggtagcctgctttcgagactggtgaagacttttgtaatggtcatgactcatg-attggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
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gagaataatccactgttctaccttttcttgta--ttgccct-gcaacatatggctgctct-atgtctttcctggcaaattcaataaactcttgctgttgtccagGTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG
upper sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 3
agaaaagtaataacatatattcgagggtagcctgcttt-cgagactggtgaagacttttgtaatggt-catgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
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--tattgttgttgtatttgttttgaaatatgatgatgagcaagattgccttgtgcttgttcatttatgcttgattatttatctcctgaatttcatgtatcagGTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAG
upper sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G28170.1 (Glycine max), 3'ss of exon 3
agaaaagtaataacatatattcgagggtagcctgct--ttcgagactggtgaag-acttttgtaatggtcatgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
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-gaaatatactaagtta-ataagattgtgctgtgcttgttcatttatgctctattatttatctgcataccaatgtctat-atctccttcatttcatgtatcagGTGATGGGAGAGTATGGCTATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCCG
upper sequence: AT5G51570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 3'ss of exon 3
-----agaaaagtaataacatatattcgagggtagcct---gctttcgagactggtgaagacttttgtaatggtcatgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
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ctttctatcttctgccattgcataactgaacaaaattttgtgcactaaaagcaactttatttttctaaaatatctatta--tatg-ttgaaaacatggat-----cagGTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGMapped 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|125190181|gb|EL205135.1|EL205135EST: CAAAAGGGTGAAGTTGCCAAGTCTGTTCTTGAGGAGCTTGAGAAG GTGATGGGTGCTTATGGATACAGCAT
genomic: CAAAAGGGTGAAGTTGCCAAGTCTGTTCTTGAGGAGCTTGAGAAGgtataacatc ... gtttcttcagGTGATGGGTGCTTATGGATACAGCAT
EST:
gi|164072856|gb|ES016749.1|ES016749EST: TTGAACAAAAGGGTGAAGTTGCCAAGTCTGTTCTTGAGGAGCTTGAGAAG GTGATGGGTGCTTATGGA
genomic: TTGAACAAAAGGGTGAAGTTGCCAAGTCTGTTCTTGAGGAGCTTGAGAAGgtataacatc ... gtttcttcagGTGATGGGTGCTTATGGA
EST:
gi|124960306|gb|EL034983.1|EL034983EST: CAAAAGGGTGAAGTTGCCAAGTCTGTTCTTGAGGAGCTTGAGAAG GTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATT
genomic: CAAAAGGGTGAAGTTGCCAAGTCTGTTCTTGAGGAGCTTGAGAAGgtataacatc ... gtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgaagacttttgtaatggtcatgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
ttgtttgtttcttc CT-rich tract
ttttgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaaagtaataacatatattcgagggtagcctgctttcgagactggtgaagacttttgtaatggtcatgactcatgattggagttgtttgtttcttcagGTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAG
agaaaag
- - - - aataaca
- - - - - - - - - - - - - - - -ctgcttt