Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaccaatatgcaaagctcttttatgcattcctcaaaagttacaaactttgataatgcaaattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAGAGTGAAAAATTGGATGACGTTCAACGAGCCGCGTGTGGTAGCTGCTTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g32364.1 (Oryza sativa), 3'ss of exon 5
--gtaagcaccaatatgcaaagctcttttatgcattcctcaaa----agttacaaac--tttgata-atgca------------------aattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAGAGTGAAAAATTGGATGACGTTCAACGAGCCGCGTGTGGTAGCTGCTTTA
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ttttaacaatcaccatgcagcagcagattgtgcattcctgaaactgtagatcaagatgatccaatatatgtatctactggtttgtttttgaatcacgcagGGAAGCATTCGCAGACTACGCTGAGTTTTGCTTCAAGACATTTGGCGACAGAGTGAAGAACTGGATGACATTTAACGAACCGAGAGTTGTTGCCGCTCTA
upper sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 5
---------------------------gtaagcaccaatatg-caaagctcttttatgcattcctcaaaagttacaaactttgataatgcaaattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAGAGTGAAAAATTGGATGACGTTCAACGAGCCGCGTGTGGTAGCTGCTTTA
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tttctcagattaatatttgaagtttgtttgataaaaagtatatcttaacatgcttataatgcaactatgtgtaactaacatgaatgct-tgaattgtacagGAAAGATTTTGCAGATTATGCAGAATTTTGTTTCAAGACTTTTGGAGATAGAGTTAAGAATTGGATGACGTTTAACGAACCTCGTGTGGTGGCTGCTCTT
upper sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------gtaagcaccaatatgcaaagctcttttatgcattcctcaaaagt-------tacaaactttgataatgc--aaattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAGAGTGAAAAATTGGATGACGTTCAACGAGCCGCGTGTGGTAGCTGCTTTA
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gtaagtaccaatatatatacaagagcaaaaatggattattgatcttttgaatacatgttttctcatagattaatatttgaagtttgaagtatatgttagcatgcttacaatgcaattctgcataactaatgtgaatgcttaaattgtacagGAATGATTTTGCAGATTATGCAGAATTTTGTTTCAAGACTTTTGGAGATAGAGTTAAGAATTGGATGACGTTTAATGAACCTCGTGTGGTGGCTGCTCTTMapped 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|125111473|gb|EL162939.1|EL162939EST: AAAACAAGTATAAAGGCTTGCTTGGTAGACAAGTAGT GAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAG
genomic: AAAACAAGTATAAAGGCTTGCTTGGTAGACAAGTAGTgtaagcacca ... aattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcttttatgcattcctcaaaagttacaaactttgataatgcaaattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAGAGTGAAAAATTGGATGACGTTCAACGAGCCGCGTGTGGTAGCTGCTTTA
ctttgat putative branch site (score: 5)
ataatgcaaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaccaatatgcaaagctcttttatgcattcctcaaaagttacaaactttgataatgcaaattttacagGAAAGATTTTGCGGATTACGCTGAGTTTTGTTACAAGACATTTGGTGATAGAGTGAAAAATTGGATGACGTTCAACGAGCCGCGTGTGGTAGCTGCTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT