Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07290.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggttt-agGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
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gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 11
--------------gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
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aaattttagaggcagtaaa-gaattcatactctcttgcattagtctcccgatttgacttgtttctgtttttttatttatt--tatttgctatttgtttggta--------gGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 7
---gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtt-tagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
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tacaaaatttgaataacaatttttaaaaacaagcaaattcttttgcactggtctttcagtttgtctctttc-atttatatttgtttaaatatttttggcagGTATACTTCAAAGATGCTTCTTGTTGCCATAGATGAGCAATGTCGAGGAACTTATGATTTTCTGTATTTGCCAATTGATTTCAAG
upper sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
-----gtaagtgaattcaccttttctccctattattccctg---ttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
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cattcatttctatttgtggttttacacaccataattgctcagattcctgttgcatcctctgttatttctgccttttgatttga---tataatggtaattgt--agGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAAMapped 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|116455509|gb|EG498101.1|EG498101EST: CGTGGGGAAGACAGTAGAACAACGTTGATGATAAAGAACATTCCTAATAA GTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAAC
genomic: CGTGGGGAAGACAGTAGAACAACGTTGATGATAAAGAACATTCCTAATAAgtaagtgaat ... aatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
ttataac putative branch site (score: 2)
tatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggtttagGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA