Sequence
atgc intronic sequence ATGC exonic sequenceatatccttactatgcaatatcccatataatgtgatattatgctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 6
atatccttactatgcaatatcccatat----aatgtgatattatgctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
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atatcctgtctatgaaatatcttatattttcatttttttactatgttgacttcatttaatatattttaa-------atccttaactgcatgacacGTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT
upper sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 6
atatcctt-actatgcaatatcccatataatgtgatattatgctctattcatcaattgcacttttatgttattat-ccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
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atatccttcactacataatgc----ttttgtat-atatcgc-ttatacttgtcaacaaaag----atattgtgataccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
upper sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G76170.1 (Arabidopsis thaliana), 3'ss of exon 6
atatcctt-actatgcaatatcccatataatgtgatattatg-ctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
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atatcctttgctattaaatcttttgttttgcttcccgaaacaactttaactgtcaacagaagatattcgtta--gaccttaacatagttacacGTATGCTTATTTCAAGAAGCTGGACTACTTCTCCACTGAAT
upper sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G44270.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------atatccttactatgcaatatcccatataatgtgatattatgctctattcatcaattgcactttt---------atgttattat-ccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
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gtatacatacgaaaaggagattgtcatatatccttcactacataatgcttt--tgtatatatcgcttatacttgtcaacaaaagatattgtgataccttaacgtagCTTTACGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
upper sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 6
atatccttactatgcaatatcccatataatgtgatattatgctctattcatcaattgcacttttatgttattat-ccttgaccttatg-acacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
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--------gttgtg----gttgagttttttgttatatgttattcagattattatttctttctgtaagCTGCAAAACCTTAACCGGATTTACACGTATGCATATTTCAAAAGGCTAGACTACTTTTCCACCGAATMapped 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|218487495|gb|FG946534.1|FG946534EST: ATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTAT GTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
genomic: ATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTATatatccttac ... cttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
EST:
gi|29640585|gb|CB645594.1|CB645594EST: ATCCCAAGATGCAAGCCTTTCAAATACACTTACGAGAAGGAGATTGTTAT GTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
genomic: ATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTATatatccttac ... cttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
EST:
gi|218488923|gb|FG954497.1|FG954497EST: ATCCCAAGATGCAAGCCTTTCAAATAC-CCTATGAGAAGGAGATTGTTAT GTATGCCTATTTCAAAAAGCTGGACTACTTCTCCACAGCAAT
genomic: ATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTATatatccttac ... cttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAG-AAT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
47 (upstream exon),
29 (downstream exon)
Score:
1GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTATatatccttac ... cttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
atccttgac putative branch site
acttttatgttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatccttactatgcaatatcccatataatgtgatattatgctctattcatcaattgcacttttatgttattatccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA