Sequence
atgc intronic sequence ATGC exonic sequencegtatagttctgaatatagttcactgtttaacaagtctaaggctagctcttatcttcattctcattactcacttgttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAACTTACTTTTCTACAGCATTTTCGATGTGGGATGCAGATTTCTATGTCAAAGTAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
-------------------------------------------gtatagttctgaa--tatagttcactgtttaacaagtctaaggct-agctcttatcttcattctcatta-----ctcacttgttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAACTTACTTTTCTACAGCATTTTCGATGTGGGATGCAGATTTCTATGTCAAAGTAGATG
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gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 5
--------------------------------gt-atagttctgaatatagttcactgtttaacaagtctaaggctagctctta-tcttcattctcattactcac--ttgttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAACTTACTTTTCTACAGCATTTTCGATGTGGGATGCAGATTTCTATGTCAAAGTAGATG
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gtaagttaattccttgttgctcttgcgcaggagtgatacatgtgaactttgttctgagttttgctcag--acggctgggttttcctccatattcacagtggctacaatttttttgttcagGATCATGTTGAAGGGTACCTTGCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACGMapped 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|125069562|gb|EL135295.1|EL135295EST: CAGGAAGCATGGAGATTTCTTGAGACTG GACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAA
genomic: CAGGAAGCATGGAGATTTCTTGAGACTGgtatagttct ... ttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagtctaaggctagctcttatcttcattctcattactcacttgttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAACTTACTTTTCTACAGCATTTTCGATGTGGGATGCAGATTTCTATGTCAAAGTAGATG
tactcac putative branch site (score: 1)
ctcacttgtttttt CT-rich tract
acttgttttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagttctgaatatagttcactgtttaacaagtctaaggctagctcttatcttcattctcattactcacttgttttttatagGACCATGTTGAAGGGTACCTAGAGTTGTCAGGCAAGACGAAAACTTACTTTTCTACAGCATTTTCGATGTGGGATGCAGATTTCTATGTCAAAGTAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT