Sequence
atgc intronic sequence ATGC exonic sequencegtatatatacactcttaaccttatgctgaaaagtttctttactcggtggagaagactaaatttgtgacaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12280.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
gtatatatacactcttaaccttatgctgaaaagtttctttactcgg-tggaga--agactaaatttgtg---acaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
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gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G016997_T01 (Zea mays), 3'ss of exon 14
gtatatatacactcttaaccttatgctgaaaagtttctttactcggtggagaagactaaatttgtgacaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
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--gttagttctgtcttgtttttagcttttaagaatttcgcgatgagttg-gaagtttatatgactgaattatatcctgccagAAAACAGGAGAAGATCATGTTGATATTATCACTTTCTACAATGAAGTATTTATTCCTGCTGTCAAGCCTTTGTTAGTGGAGGTTGGACCTGGTGCTAGTC
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 15
gtatatatacactcttaaccttatgctgaaaagtttctttactcggtggagaagactaaatttgtgacaatg-acttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
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gtaagttccta-tcttgttttcaacttatataagaattttggaatgagtcgaaagtctatctgatcaaattgtatcctgccagAAAACAGGAGAAGACCACGTCGACATCATCACTTTCTACAACGAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCG
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G36890.1 (Glycine max), 3'ss of exon 14
gtatatat---acactcttaaccttatgctgaaaagtttctttactcggtggagaagacta-aatttgtgacaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
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gtatgcaactgaaggtcaaaattcaatgcttatgtttaacttttctgagaattgttactcacaactgatctgaatga---aaacagAGAACAGGACAGGATCATGTTGACATCATTACCTTTTACAATGAAATATTCATTCCTTCTGTAAAGCCACTGCTGGTTGAACTTGGCCCTGCTGGACCAA
upper sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv04s0008g02780.t01 (Vitis vinifera), 3'ss of exon 14
gtatat-atacactcttaaccttatgctgaaaagtttctttactcggtggagaagactaaatttgtgacaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
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gtatgttgcttaatctctattctcttagtgttagcttc--tgttctatgg-gaaatctaagcctttcaactgattttgaacagAAAACAGGGAAGGAACATGTTGATATTATCACATTTTACAATGAAATTTTTATTCCGGCTGTAAAGCCGCTGTTAATGGAGATTGGGCCTGGTGGTGGAAMapped 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|163966338|gb|ES177628.1|ES177628EST: GTGGATGCGTTACAATGTCGCCGTCAAGGG AGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTT
genomic: GTGGATGCGTTACAATGTCGCCGTCAAGGGgtatatatac ... acttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaagtttctttactcggtggagaagactaaatttgtgacaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
gactaaa putative branch site (score: 2)
actaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatacactcttaaccttatgctgaaaagtttctttactcggtggagaagactaaatttgtgacaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA