Sequence
atgc intronic sequence ATGC exonic sequence...ctagacctcctgctcaaaccctagattagttacaaatagtcatttactagacttaacaagaaagccttgtctgacttcctgacgcttaaaatatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAACGTGCTATTGAACTAGGAGCAGGTTGTGGCGTTGCAGGATTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08125.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08125.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G19970.2 (Glycine max), 3'ss of exon 4
ctagacctcctgctcaaaccctagattagttacaaatagtcatttactagacttaacaagaaagccttgtctgacttcctga----cgcttaaaatatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAACGTGCTATTGAACTAGGAGCAGGTTGTGGCGTTGCAGGATTTG
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--agatcctttgaagatgaactaggaca--tgaaattctttatcttgtaatattctaaattcacattatcttgatttcttagggtgcatcttatattgtttcagGAACGGAATTGCAGAAAGGGAAGGTTTTCCCCAGCTAAACTTAAAGGAAAACGTGTAATTGAACTAGGAGCTGGTTGTGGTGTTTCTGGTATTG
upper sequence: AT1G08125.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0061g00490.t01 (Vitis vinifera), 3'ss of exon 5
ctagacctcctgctcaaaccctagattagttacaaatagtcatttactagacttaacaagaaagccttg--tctg---acttcctgacgcttaaaatatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAACGTGCTATTGAACTAGGAGCAGGTTGTGGCGTTGCAGGATTTG
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--ctgcaatctgcatgggtcatgagttgtggacttaca-ttgctttctgtgtgatactgtattcttctaaatctgcaaagttgcacttgtttgaatcact--cagGAGAGGAATTGCAGAAAGGGAAGGTTTAGCCCATCTAAATTGAAAGGAAAACGTGTTATTGAACTTGGAGCAGGTTGTGGAGTAGCTGGATTTG
upper sequence: AT1G08125.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv03s0017g01120.t01 (Vitis vinifera), 3'ss of exon 5
ctagacctcctgctcaaaccctagattagttacaaatagtcatttactagacttaacaagaaagccttg-tctg---acttcctgacgcttaaaatatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAACGTGCTATTGAACTAGGAGCAGGTTGTGGCGTTGCAGGATTTG
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--ctgcaatctgcatgggtcatgagttgtggacctacattgctttctgtgtgataccgtattcttctaaatctgcaaagttgcacttgtttgaatcact--cagGAGAGGAATTGCAGAAAGGGAAGGTTTAGCCCATCTAAATTGAAAGGAAAACGTGTTATTGAACTTGGAGCAGGTTGTGGAGTAGCTGGATTTGMapped 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|152035663|gb|BP860254.2|BP860254EST: ATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTG GGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAA
genomic: ATTTAGGAACGACCGTGTGGGATGCGTCCATGGTGTTTGCCAAATATCTGgtataaatag ... atatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagacttaacaagaaagccttgtctgacttcctgacgcttaaaatatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAACGTGCTATTGAACTAGGAGCAGGTTGTGGCGTTGCAGGATTTG
tcctgac putative branch site (score: 2)
ttaaaatatttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagacctcctgctcaaaccctagattagttacaaatagtcatttactagacttaacaagaaagccttgtctgacttcctgacgcttaaaatatttacagGGGAAAAATAGCAGGAAGGGAAGGTTTAGTTCATCTAAACTGAAAGGGAAACGTGCTATTGAACTAGGAGCAGGTTGTGGCGTTGCAGGATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
ctagacc
- - - - - - - caaaccc
- - - - - - - - - - - - - - - -acaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaaa