Sequence
atgc intronic sequence ATGC exonic sequencegtatcgaagagtaaccaagaaaagtatgacatttttatcaaagaagatattggttctcttgattctgaaatctgcatttccagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g41020.1 (Oryza sativa), 3'ss of exon 5
------gtatcgaagagtaaccaa--gaaaagtatgacatttttatcaaa----gaa--gatattggttctcttgattctgaaatctgcatttc---cagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
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cagtgtgtgctttcttgcaaataattgtacacttcaatacttgtggtgaaacttgaatgaatcttggtgcatctgaccataagtcctatttatgaaacagGAGATTGCAACATTCTTCATGGACATAGTTAATTCTTCTCATAGCTATGCCACTGGTGGCACATCTGTCAGTGAGTTCTG
upper sequence: AT5G12950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G14020.1 (Glycine max), 3'ss of exon 5
---------gtatcgaagagtaaccaagaaaagtatgacatttt--tatcaaagaagatatt--ggttctcttgattctgaaatctgcatt-----tccagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
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tgtatatttgtattgga-agtaatcattaagcccagcacaacttaatatttgtcatgcctttcaaatttctgagatttgttcgtgtttattggtgttttagCAAATTGGGACATTCTTTATGGACCTCGTAAACTCTTCTCACAGCTATGCAACTGGAGGGACATCAGTCAGCGAGTTCTG
upper sequence: AT5G12950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G05970.1 (Glycine max), 3'ss of exon 8
gtatcgaagagtaaccaagaaaagtatgacattt-ttat-caaagaagatattggttctcttgattctgaaatctgcatttccagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
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gtatcattgtatagcccagcacaacatagcatttatcatgcctttcaactttcggagACCTGTGCTTGTTTATTGGTGTT---ATGAAATTGAGACATTTTTTATGGACATCGTAAACTCTTCTCACAGCTATGCAACAGGAGGGACATCAGTCGGCGAG-----
upper sequence: AT5G12950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G05980.1 (Glycine max), 3'ss of exon 5
---------gtatcgaagagtaaccaagaaaagtatgacatttt--tatcaaagaagatattggttctcttga-------ttctgaaatctgcatttccagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
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tgtagatttgtgttgga-agtaatcattaagcccagcacaacttaatatttgtcatgcctttcaactttctgagactttttcttgtttattggtcttttagCAAATTGGGACATTCTTTATGGACCTCGTAAACTCTTCTCACAGCTACGCAACTGGAGGGACATCAGTCAGAGAGTTCTGMapped 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|125131109|gb|EL173927.1|EL173927EST: GATCCCAACAACGGTATGAAATCACTGGTGATCTACTCCATAAG GAAATCTCGATGTTCTTTATGGACATTTTTAA
genomic: GATCCCAACAACGGTATGAAATCACTGGTGATCTACTCCATAAGgtatcgaaga ... gcatttccagGAAATCTCGATGTTCTTTATGGACATTTTTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttttatcaaagaagatattggttctcttgattctgaaatctgcatttccagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
tcttgat putative branch site (score: 4)
catttcc putative PPT
tttatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcgaagagtaaccaagaaaagtatgacatttttatcaaagaagatattggttctcttgattctgaaatctgcatttccagGAAATCTCGATGTTCTTTATGGACATTTTTAATGCTTCTCACAGCTATGCAACAGGAGGAACATCAGTCAGTGAGTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA