Sequence
atgc intronic sequence ATGC exonic sequenceGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04170.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 5'ss of exon 3
GAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
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GTACCATTGGGCATGTGGCCCATGGAAAGTCCACCGTTGTGAAAGCTATATCTGGAGTTCAGgtataattcatatatttcattattgcacttctt-tccaagtgatgaatctagact-ctgtgtatacctga--gaattatatc---tcacgtttatcagtaacttttc------------
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 5'ss of exon 3
GAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
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GTACCATAGGGCATGTGGCCCATGGAAAGTCCACTGTTGTGAAGGCTATATCTGGAGTTCAGgtattattaatgtattttattatcatgcttctt-tccgagtgatgaatctgaact-ctgcgtatacctgac--aactatgta---tcacatttattggtaacctgtg------------
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 3
GAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
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GTACCATTGGCCATGTGGCTCATGGAAAGTCCACTGTTGTTAAAGCTATATCTGGTGTTCAGgtgtgattcatgtattccagtgtaatatttgtt-tcaaacattgaatccgagttttgtatttggtgtcaatttta-tgtgtcatct---ttctgtatcttttttt--------------
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G117900_T01 (Zea mays), 5'ss of exon 3
GAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttg-atcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
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GTACCATTGGCCATGTGGCTCATGGAAAGTCTACTGTTGTGAAGGCTATATCCGGAGTTCAGgtgtgattcacatattctagtataatatttgtt-ttcaagcattgggtccaagtcatgtctttggtgtcagtttta-tgtgtcatct---ttctgta-tctgctta--------------
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 5'ss of exon 2
GAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
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GCACAATTGGTCATGTGGCTCATGGGAAGTCCACAGTTGTAAAAGCTATATCTGGTGTTCAGgtgttttttttttttttttgggtttcttttttgaatttaacactgctttttattagttttatttctttagaagagttgagtgtaa--atttgtattgtcacc-----------------Mapped 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|164146805|gb|ES184847.1|ES184847EST: ATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG ACTGTACCGTTT-AAAAATGAATTGGAGCGTAACATTACCATTAAG
genomic: ATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttg ... ctctgtacagACTGT-CCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacag
- - - - - - - - - - CATGGA