Sequence
atgc intronic sequence ATGC exonic sequencegttttactttttcccctttccccatctcgatttctgatttgcgtttgattcaactcaagtttcatcgctgaaacgcccgtgtgtttgcttgcgaatcccctccagGTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g52470.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S138_93V6.1 (Physcomitrella patens), 3'ss of exon 1
gttttactttttcccctttccccatctcgatttctgatttgcgtttgattcaactcaagtttcatcgctgaaacgcccgtgt-gtttgcttgcgaatcccctccagGTTGCCAAGAT-GGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG
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------------------aggcggtgtgggtatc-gtggggtttttggtccgattggagtttcctattagggcgaagtgtttcatgttctgatggattggtgcgctcgtgttgtgacagGTGAAGTTTTCGGCGGACGAGCTCCGCGCCATCATGGACAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACG
upper sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ28367 (Selaginella moellendorffii), 3'ss of exon 1
gttttactttttcccctttccccatctcgatttctgatttgcgtttgattcaactcaagtttcatcgctgaaacgcccgtgtgtttgcttgcgaatcccctccagGTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG
||| | ||| || | || | || || | | | || |||| || ||||| || ||||| ||| || |||||| |||||| ||||||||||||||||||||||||| || || || ||||| |
------------------------------------------------------gtgagtgattcctctggaattc----gtagcggattctgacatcgtgatgctctttccag-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|88400823|gb|CI616828.1|CI616828EST: CTGACATCTCCTTCCTCTCCCCCTTCGCCTGCGCCTCTGCTCCTCGTCAG GTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGAT
genomic: CTGACATCTCCTTCCTCTCCCCCTTCGCCTGCGCCTCTGCTCCTCGTCAGgttttacttt ... tcccctccagGTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactcaagtttcatcgctgaaacgcccgtgtgtttgcttgcgaatcccctccagGTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG
tcccctcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttactttttcccctttccccatctcgatttctgatttgcgtttgattcaactcaagtttcatcgctgaaacgcccgtgtgtttgcttgcgaatcccctccagGTTGCCAAGATGGTGAGGTTTACGGCGGAGGAGCTCCGCGCGAGCATGGATAAGAAGGACAACATCCGGAACATGTCTGTGATCGCGCACGTTGATCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG