Sequence
atgc intronic sequence ATGC exonic sequence...tgaataccacttccattgttacatgaaaaactgtgaagtaatttgtacactgattttctaaatccatgactagattattttacacaaataatgcttccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04660.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G174343_T07 (Zea mays), 3'ss of exon 3
tgaatac-----cacttccattgttacatgaaaaactgtgaagtaatttgtacactgattttctaaatccatgactagattattttacacaaataatgcttccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
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taaatgtttttacagctatgtttttttacccatgacttttgctggtataaaataccggt--tctagac---tgtcaacaatttctcacagtatttccattgccagGGTCTTTTGCTGGTCTTGGATTTTTGTCACTCTACCTGTCAGGCAAAATTAAGGCCTTCAATCGCCAAGGTCACGTGGCCAAACTTTGCATAGTGATCCT
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G09820.1 (Glycine max), 3'ss of exon 5
------------------------------------------tgaataccacttccattgttacatgaaaaac-tgtgaagtaatttgtaca-ctgattttctaaatccatgactagattattttaca-----------caaataatgct--------tccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
|| | ||| | |||| | | || || | |||| || | || ||| || | | ||| ||| | ||||||| | |||||||||||||||| || || ||| | ||| | ||| ||||||| ||||| || | ||||||||| ||||||||||||| |||||||||||| | || |
gtatgtagcatttagttcatgtgttatttgtacagaggtctacaaaaaagactggctttgtcatgctcataatgcatggtggaattagtttagctcattcaaagcatgtgtactcaaatttctttttagttgtttgttttaaataatttcaatttatgtgcagGGTCTTTTGCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTAT
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA18G53100.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------tgaataccacttccattgttacatgaaaaactg-tgaagtaatttgtacac-tgattttctaaatccatgactagattattttacacaaataatgct--------tccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
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gtatgtagcatttatttatttcatgtactctttgtacataggtctagtaacttttctgtacttcatttcaatagaaatgaatggtggaatcagtttaggttattctactcaaattttattctattgtttgctttaaatattttcaatttatgtgcagGGTCATTTTCTGGTCTGGGTTTTTTATCATTGTACTTATCTGGAAAAATAAAAGCATTTGATCGCAAAGGTCATGTTGCAAAACTTTGCATTGTTTTTCTMapped 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|16575632|gb|BI802928.1|BI802928EST: ATGGAC-CAAGAGTTTTCCTAGTGGACACACGTCGT GTTCTTTTGCTGGACTTGTATTTCTGTCACTCTACCTATCTGGCAAAATTA
genomic: ATGGACGCAAGAGTTTTCCTAGTGGACACACGTCGTgtaagtttgt ... atgcttccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTA
EST:
gi|218497722|gb|FG949370.1|FG949370EST: AAGCTTCTTAAAGGATGGACGCAAGAGTTTTCCTAGTGGACACACGTCGT GGTCTTTTGCTGGACTTGTATTTCTGTCACTCTACCTATCTGGCAAAATTA
genomic: AAGCTTCTTAAAGGATGGACGCAAGAGTTTTCCTAGTGGACACACGTCGTgtaagtttgt ... atgcttccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacactgattttctaaatccatgactagattattttacacaaataatgcttccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
ttctaaa putative branch site (score: 2)
tgcttcc putative PPT
tagattattttacaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaataccacttccattgttacatgaaaaactgtgaagtaatttgtacactgattttctaaatccatgactagattattttacacaaataatgcttccagGGTCTTTTGCTGGACTTGGATTTCTGTCACTCTACCTATCTGGCAAAATTAAGGTGTTTGATCGCCAAGGTCATGTTGCCAAACTTTGCATTATGATTCT
- - - - - - - - - ttacatg
- - - - - - - - - - - - -aaaaactg
- - - - - - - - - - - - - - - - - - - - - -tgtacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaata