Sequence
atgc intronic sequence ATGC exonic sequence...aggataaagtttcagttttgtgtttcgtttgattgatcttattgtcttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G18150.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 1
aggataaagtttcagttttgtgtttcgtttgattgatcttattgtcttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG---
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ggcacaaggtttcgttcccaagaaatatgtcatcaacccgttcatacc-acctagcattcagtactgttactatagtgaactttaccttcttccattccagG--AACCTGACTTCTTCACTGAATATGGTGAAGCAAACCGGTATAAAGTCAGTGAAGTCATTGGCAAAGGGAGTTATGGTGTTGTGGCTGCCGCTGTCGACA
upper sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 1
----------aggataaagtttc-----agttttgtgtttcgtttgattgatcttattgtcttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
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gattttatgctgaatagagattgtagtaggtcacaagaagagatccaatgaagttatagtcttcaaattatgtttctaatggtttctggtg---atca--agcagGGTGCACCAGAG----ACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG------
upper sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 1
------aggataaagtttcagttttgtgtttcgtttgatt-gatcttatt--gtcttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
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gattttatgctgaatagagattgtagtaggtcaaaagaagagatccaattaagttatagtcttctaattatttttctaatggtttctggtgatcaagcagGGTGCACAAG---AGACAGAGTTTTTTACCGAGTACGGGGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTCGTGGGTTCTG------
upper sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 1
aggataaagtttcagttttgtgtttcgtttgattgatcttattgtcttgatccatcatt--ttggtcaattttaagtatgaatcatgaataaaattc-ttcagGGT------GAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
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aaaaaaaatattttcttctccattctgt---actaattcaaccatttatatacttgattaattgataaataatgattgctaagggagaccattttttactcagGGCATGCCAGAAACAGAATTCTTCACAGAATATGGAGAGGCGAGCAGATACCAAGTCCAGGAAGTTGTTGGCAAAGGAAGTTATGGTGTTGTTGGCTCTG------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|124732808|gb|EH824210.1|EH824210EST: CCTAAACGTAATCATTTACCTGTGGATCCTCACAAGAAG GGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATT
genomic: CCTAAACGTAATCATTTACCTATGGATCCTCACAAGAAGgtacctttct ... aattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
tcttgat putative branch site (score: 4)
ttcttc putative PPT
aattttaagtatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggataaagtttcagttttgtgtttcgtttgattgatcttattgtcttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT