Sequence
atgc intronic sequence ATGC exonic sequencegtaagcacagtcttcattttcattcctttgtttattaatttcaatgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50430.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
-----gtaagcacagtcttcattttcattcctttgtttattaatttca--atgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
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tgactgtaagc-tattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggat--ttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
upper sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 6
gtaagcacagtcttcattttcattcctttgtttattaatttca--atgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
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gtaagc-tattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggat--ttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
upper sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
gtaagcacagtcttcattttcattcctttgtttattaatttcaatgaacttgtctgttatctaattagctttatcattcca--tcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
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gtaagttctcttttctgttgtagcacaaaaca-attagtatca-tgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
upper sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 7
gtaagcacagtcttcattttcattcctttgtttattaatttcaatga-acttgtctgtt-atctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
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gtaagtct--cttgctgtttcatagatggaaaatcctttcttatttatatttagaagttgattttattttcacttttattctgttact---tttccagTTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG
upper sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ16846 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcacagtcttcattttcattcctttgtttattaatttcaatgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
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---------------------------------gtaagcatcaa-gcgcttgtttttgctctcattg--tgtgttcttct-----------cgcagTTCATCCAGAGACTTGGAATCCAATGTGGTCAGTTTCAAG
upper sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ32150 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcacagtcttcattttcattcctttgtttattaatttcaatgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
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---------------------------------------------gtaagcatcaatcgcttatttctcctc-tcattgtgt-gttcttctcgcagTTCATCCAGAGACTTGGAATCCAATGTGGTCAGTTTCAAGMapped 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|86068907|gb|DR364664.1|DR364664EST: AAATGGTCGATTTGTGACGCAAAAGAAAATCTGCTTGTCTATGAGTGACT TTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
genomic: AAATGGTCGATTTGTGACGCAAAAGAAAATCTGCTTGTCTATGAGTGACTgtaagcacag ... ccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
atctaat putative branch site (score: 3)
tcattcc putative PPT
ttatctaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcacagtcttcattttcattcctttgtttattaatttcaatgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA