Sequence
atgc intronic sequence ATGC exonic sequencegtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g01630.6 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
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----------------------------------------------gttcctacttttctgaatcttatgagatt-gctgtatagtgggtc------atgatttctcctaaattattctcactga----tacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G03930.1 (Glycine max), 3'ss of exon 6
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
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-----------------------------------------------gttcctactattttaatcttatgagatt-gctgtatagtgggtca--tgatttctcctaa--------attattcccaatgatattcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
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---------------------------------------------gcat-gtacctctgaatacctcttacgaaaattaacatggtttattgtttta--tcattctacta-aagatatctgttgaaa---cttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 7
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
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---------------------------------------------gcat-gtgcctttctgaagctatgagaatacaaaccatgctcaatttactgttttatgattga-atgttttgtttatcaaa-----tgcagGGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACTMapped 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|58669994|gb|CK058680.1|CK058680EST: CTTCACTCTCCCCTACCATGACTGAG GGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGT
genomic: CTTCACTCTCCCCTACCATGACTGAGgtacaatact ... ttgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
tcaaacttattaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT