Sequence
atgc intronic sequence ATGC exonic sequencegtatgcgaaattgcatatggcattcctcgtgcatctcgatattgcttaattgtggattgattgcttttatgacttgaatgacagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTAGGACAACTGGTGTCGAAGGAAGGATCATAAATGTGTCGTCTTCGGGGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g40030.6 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g40030.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G464885_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------------------gtatgcgaaattgcatatggcattcctcgtgcatctcgatattg---cttaattgtggatt---gattgcttttatgacttgaatgacagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTAGGACAACTGGTGTCGAAGGAAGGATCATAAATGTGTCGTCTTCGGGGCA
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gtgtgtcctcttataccagtacacactacagctagcctttgctaagcgtattgttcgaattctaactactttctttgtgcgacatctcttgtttacattattctgtagaagagtatcccttgctcgtcttatgacctatgagaatgattcctgataatgcactagcgattaaccgggatatatatatggcagGCCATTTTCTTCTAACGAACCTCTTGCTAGAAAACATGAAGAAGACATGTAGGGACAGCGGTATCGAGGGACGGATTGTCAATTTGACATCTTCGGCGCA
upper sequence: LOC_Os10g40030.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G128577_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------gtatgcgaaattgcatatggcattcc-----tcgtgcatctcgatattgcttaattgtggattgattgcttttatgacttgaatga---cagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTAGGACAACTGGTGTCGAAGGAAGGATCATAAATGTGTCGTCTTCGGGGCA
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gtgtgtgtcattagcccaaaaattattcgaaccgcgatttcgttttgcagcgcgtcttgtttaatctacctcactttcggcacttgaattatgatgtatgagaacgattcctgctggtactgtagcagcatt--agacttgaatggtggcagGTCATTTTCTTCTAACAAACCTCGTACTGGAGAACATGAAGAGCACGTGCAGGGACACAGGCACCGAGGGACGGATCGTCAATGTGACATCTGCAGGGCAMapped 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|29656760|gb|CB653035.1|CB653035EST: CATACGCTCCATTGACGGCCTAGAATTGCATTTTGCAACTAATCACATTG GCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTA
genomic: CATACGCTCCATTGACGGCCTAGAATTGCATTTTGCAACTAATCACATTGgtatgcgaaa ... tgaatgacagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTA
EST:
gi|38471413|gb|CF955544.1|CF955544EST: CATACGCTCCATTGACGGCCTAGAATTGCATTTTGCAACTAATCACATTG GCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTA
genomic: CATACGCTCCATTGACGGCCTAGAATTGCATTTTGCAACTAATCACATTGgtatgcgaaa ... tgaatgacagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatctcgatattgcttaattgtggattgattgcttttatgacttgaatgacagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTAGGACAACTGGTGTCGAAGGAAGGATCATAAATGTGTCGTCTTCGGGGCA
gattgat putative branch site (score: 4)
ttaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcgaaattgcatatggcattcctcgtgcatctcgatattgcttaattgtggattgattgcttttatgacttgaatgacagGCCATTTTCTTCTAACGAATCTTTTACTGGAGAACATGAAGAGCACAAGTAGGACAACTGGTGTCGAAGGAAGGATCATAAATGTGTCGTCTTCGGGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA