Sequence
atgc intronic sequence ATGC exonic sequenceGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g01630.6 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G03930.1 (Glycine max), 5'ss of exon 7
GGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattag
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GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACTgtatggt--tcttgaaccagagttaacatggcatg-taaaataccactattaagattcttatgtgaacattgtcatctaaat-gtatttcatatttcatatgaag--
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G00590.1 (Glycine max), 5'ss of exon 7
GGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattag
|| ||||||||||| ||| ||||||||||||| |||| | |||| ||||||||||| || |||||||| || |||||| | | | | | | || | | || | ||| | ||| | || | || || || || || | ||| |||| |||
GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACTgtatggt--tcttgaaccagagttaacatggcatg-taaaataccactattgagattcttatgtgaacattgtcatctaaat-gtatttcatatttcatatgaag--
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 5'ss of exon 8
GGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattag
|| |||||||| |||||| ||||||||||||| |||||||| | ||||||||||| ||||||||||| || ||||||| | | || | || | | | || || ||| | | ||| || | | | ||||| | |
GGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACTgtaa-tgataatcctgat---tgaatctcttcctgtattgattcttatgccaggaataa--aacacttatctcaatcttaatattttag------------------
upper sequence: LOC_Os06g01630.6 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 8
GGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttactt----tcttaatgtgcacaccaag-------acttgatttaatttccctactt--tatttaattaaggagcaacagcagc-ttaaccatcaatcacatttatggtgattag
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GGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACTgtagggcccttgtactctgagtctgttggttaaattctctcaattaatggagcactccggttaggtgctttactcatctggaaaactgacgtttacctttcattgaattgatatttgtag-Mapped 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: AAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAA
genomic: AAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttact ... tggtgattagGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACTgtaagttactttcttaatgtgcacaccaagacttgatttaatttccctactttatttaattaaggagcaacagcagcttaaccatcaatcacatttatggtgattag
- - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - GGAGAT