Sequence
atgc intronic sequence ATGC exonic sequencegtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10490.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 9
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcct----gttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
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-----------------------------------gtgtgggatttatcattgcttctaaacataacaattccttgtagtttagtggccaaaatgttattgtggcacctgttgacattcaatgatattttttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G33170.1 (Glycine max), 3'ss of exon 9
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcc----tgtttta-tgctaaagatatt-tcataaaaactga-gtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
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-----------------------------------gtgtgggatttatcattgcttctaaacatcacagttcacttgtattttagtggccaaaatgttattgtggcacctgttgatgttaaatgatatttgttt--agATATTTACAAACTTCCTTTCGAGTGTGATGATTCATGCAACCCGGCCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0313g00020.t01 (Vitis vinifera), 3'ss of exon 9
--------------gtgaaacctaattctcattttaat-------tactggtttcttcggaatatccactgt-tagctttagac--gttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
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gtgcaaatttgtccatttaacacactgctatttatgaaacacacattttggttttcctgcatgcccaattatgtttcttttgccttgttccctcttcagatatggatcttacttatttca--aagcctga---tttttttgcttatcatatccagATATTCACAAATTTCCTCTCAAGTGCAATGATCCATGCAACTCGGCCTTTTGTTGTGAATGAATGGATTCAAACCAGAATTGAAGGCTATGAAGTTTCTG
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ18544 (Selaginella moellendorffii), 3'ss of exon 5
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
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-------------------------------------------------gttagatt---acgttctcctttctgttttcttcaaaacaaatgacagga-------------ttttatgttttg----tagATTTTTACGAACTTTTTGTCCAGTGTTATGATTCATGCTACCCGGCCGTTTGTTGAGTACGAGTGGATACAAACTAAAATCGATGGGCAGGAAGTTTCTGMapped 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|125066043|gb|EL133055.1|EL133055EST: TGCTGGAGGTCTTGGGACAGTTTTGATTACTCTTGCTGGCCGAGAG ATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTT
genomic: TGCTGGAGGTCTTGGGACAGTTTTGATTACTCTTGCTGGCCGAGAGgtgaaaccta ... ttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
tgctaaa putative branch site (score: 2)
tttttttttgtttttt putative PPT
atatttcataaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA