Sequence
atgc intronic sequence ATGC exonic sequencegtgattttcgctagtacatgggtgatttttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22330.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 6
-------------gtgattttcgctagtacatgggtgatttttttaagcatcttactttctcttttgcaa-ggtctaatatttttatatgccattg-tagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
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taaagtcatactcatgagttgtgtccagaaaaaaccaaaggaaaaaagaaaaggaggtacaatataaaaataagagagtaactgtttttgttggtggcagGTTGTCAACCGATATATTGATGAAGGTGTAGCAGAGCTTGTTCCTGGAGTTCTATTCATTGATGAG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 6
-------------gtgattttcgctagtacatgggtgatttttttaagcatcttactttctcttttgcaa-ggtctaatatttttatatgccattg-tagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
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taaagtcatacccatgagttctgaccagaaaaaaccaaaggaaaaaagaaaagaaggtacaatataaaaacaagagggtaactgtttttgttggtggcagGTTGTTAACCGATATATTGATGAAGGTGTAGCAGAGCTTGTTCCTGGAGTTCTATTCATTGATGAG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 6
--------------------gtgattttcgctagtacatgggtgatttttttaagcatctt-actttctcttttgcaaggtctaatatttttatatgccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
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tcttgtactcattccccactacaattttgccaag---atgataaggtccttcatgcttcctgactcataaatctcttaaatgaaatggttttgtga---atgacagGTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTCCTATTTATTGATGAG
upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------gtgatttt-cgctagtacatgggtgatttttttaag-catcttactttctcttttgcaa-ggtctaatatttttatatgccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
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gtaatttttcttgacgctgtgctgtgagtatggacaagaaacctcgtacaaagtcgtgttgtaacattatattattaatcaagaggtaatgctgagtcagaagggcaacgagtttgagatggtttctcgttcatttgtg---gtgcagGTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGMapped 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|116443983|gb|EG486575.1|EG486575EST: AACCGCGGA-GACTGAGATCACTGATA-GCT-CGGCA-GAAATTAACA-G GT-GTGA-CCGATATAT
genomic: AACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcg ... gccattgtagGTTGTGAACCGATATAT
EST:
gi|116443984|gb|EG486576.1|EG486576EST: TAAGCTTCGGCAAGAAATTAACAAG GTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTT
genomic: TAAGCTTCGGCAAGAAATTAACAAGgtgattttcg ... gccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTT
EST:
gi|164204488|gb|ES031821.1|ES031821EST: AACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAG GTTGTGAACCGATATATAG
genomic: AACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcg ... gccattgtagGTTGTGAACCGATATATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
gtctaat putative branch site (score: 3)
tctaatatttttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattttcgctagtacatgggtgatttttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT