Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaaattctttaacctttaatactttatccctcggctttttgaagttctctgtctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 3
------------gtatgcaaattctttaacctttaatactttatcc--ctcggctttt----tgaagttctct-gtctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
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tgatgcccaaacagaggtatattgttattcactatgtactgtaccaaactcagtatattcagtgcagtgctatagtgctaatatgtaattgc-aattgcagAGTATGACTCAGATGACAAGCCAATCCCTGAGACGCTTAAACCTATGGTCGATGGTGGGACTGAAGGTTTCAAAGGTCATGCTAGAGTCATCATACCTGG
upper sequence: AT5G19180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G01940.2 (Glycine max), 3'ss of exon 3
----------------gtatgcaaattctttaacctttaatactttatccctcggcttt----ttgaagttctctgtctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
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cactatctgacccctaatatgtagaatttccatctct--acattcagtcccaaagatttggcgctaattttcagtttcttgtctttttatggataaatctagAGTATGATTCTGATGATAATCCTCGAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCTTGCCAGG
upper sequence: AT5G19180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
------------gtatgcaaattc---tttaacctttaatactttatccct-cggctttttgaagttctctgt--ctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
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ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
upper sequence: AT5G19180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g02820.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gtatgcaaattctttaacctttaa--tactttatccctcggctttttgaagttctctgtctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
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gcttttgagaatcaaatgtgtgtcattttcatagtgagtagatttttctacattctgcctcatcttatctagtcgtctcattgtgtttttg-gaaatttagAGTATGATTCTGATGATAAACCACTGGAAGAAACAATTAAACCTATGGTGGATGGTGGAACTGAAGGCTTCAAGGGTCATGCCAGGGTTATCATTCCAGGMapped 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|86072230|gb|DR367987.1|DR367987EST: TTCTATCGAAGCTCGCAA-TACATCAATGGGGTAGCTTGTGGGTTTCTTG AGTATAATGAAGATGATACTCC
genomic: TTCTATCGAAGCTCGCAAATACATCAATGGGGTAGCTTGTGGGTTTCTTGgtatgcaaat ... tgaaatgtagAGTATAATGAAGATGATACTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatccctcggctttttgaagttctctgtctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
gtctgat putative branch site (score: 4)
tttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaaattctttaacctttaatactttatccctcggctttttgaagttctctgtctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG