Sequence
atgc intronic sequence ATGC exonic sequencegttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactcccttttgttctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g10290.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G818887_T01 (Zea mays), 3'ss of exon 3
gttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactcccttttgt----tctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG
|| | || | | ||||| || || | ||||| || ||| || |||| |||| | || |||| | |||| ||||||||||| |||||||||||||||||| || || ||||| || ||||| ||||||| | |||| || ||||||||||| ||||| || || || | |||
gtcaatatccttataagtgctgttt-ggttttcc----actctgaattatatgatcttaactgttttttttggggtccgttgctcatgt-tagCATCAAAGACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G062635_T01 (Zea mays), 3'ss of exon 3
gttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactccctttt---gttctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG
|| | || | | ||||| || || | ||||| || ||| || |||| |||| | || |||| | |||| |||||||||||| ||||||||||||||||| || || ||||| || ||||| ||||||| | |||| || ||||||||||| ||||| || || || | |||
gtcaatatccttataagtgctgttt-ggttttcc----actctgaattttatgatcttaactgtttttttggggtccgttgctcatgt-tagCATCAAAGCCGGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGG
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 3
gttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactcccttttgt----tctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG--------
|| | || | | ||||| || || | ||||| || ||| || |||| |||| | || |||| | |||| ||||||||||| |||||||||||||||||| || || ||||| || ||||| ||||||| | |||| || ||||||||||| ||||| || || || | |||
gtcaatatccttataagtgctgttt-ggttttcc----actctgaattatatgatcttaactgttttttttggggtccgttgctcatgt-tagcatcaaagACAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGGCAAGGATG
upper sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G063355_T01 (Zea mays), 3'ss of exon 4
gttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactcccttttgt---tctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG
|| | || | | ||||| || || | ||||| || ||| || |||| |||| | || |||| | |||| |||||||||||| |||||||||||||||||| || || ||||| || ||||| ||||||| | |||| || ||||||||||| ||||| || || || | |||
gtcaatatccttataagtgctgttt-ggttttcc----actctgaattttatgatcttaactgttttttttgggtccgttgctcatgt-tagCATCAAAGCCAGAAGAGGAGGAAGACATTCCCTCTATGGACACCTTGGACATAGGGAGATCTGATGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGGMapped 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|29638206|gb|CB643215.1|CB643215EST: CGGTGATGATGAGGACGGTGAAGGCTGGCTTGCCACACATGGAGTGCAAG CATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATA
genomic: CGGTGATGATGAGGACGGTGAAGGCTGGCTTGCCACACATGGAGTGCAAGgttgacctct ... taatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATA
EST:
gi|38477977|gb|CF962110.1|CF962110EST: CGGTGATGATGAGGACGGTGAAGGCTGGCTTGCCACACATGGAGTGCAAG CATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATAC
genomic: CGGTGATGATGAGGACGGTGAAGGCTGGCTTGCCACACATGGAGTGCAAGgttgacctct ... taatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgcactctcttttgtataggctaaactcccttttgttctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG
ggctaaa putative branch site (score: 3)
ttttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgacctctcagaatgccttgtttcagtgtttcgcgcactctcttttgtataggctaaactcccttttgttctgttggtaatgtatagCATCAAAGCAAGAAGAGGAGGAAGACATACCATCGATGGATACATTGGATATAGGGAAAACTGAAGGGATAAAGTCTATTCCCTCATATTTCAGTGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG