Sequence
atgc intronic sequence ATGC exonic sequence...ggtggtgttggttttttttttttttttgggtgggggggggggaattgtgacgatctgagtgttggtgacggtggatctgtggcgtttttgtgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g16980.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 1
-----------------------------------ggtg-gtgttggttttttttttttttttgggtgggggggggggaat-tgtgacgatctgagtgttggtgacggtggatctgtggcgtttttgtgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGT
|||| | | | || | || | | ||| ||||| | | |||||| | | || | | || ||| |||||| |||| ||| |||||||||||||||| |||||||||||| | || | | | ||||||||||||||||||| || ||||| ||||| ||||||||||
cgagctcaatccccagaggccagagccagctgctcggtgagcgccgcgcccttcgcccccctcaggccctcacgcttcgttgcttgatcgtctga-tttctctgacgggtgttttggtttggatctgggcggaccagGCGCTCCACGCGATGGCGCAGAAGGAGACCAATGGCAGCAACGGCGAGCACATCTCCACCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGT
upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165357_T01 (Zea mays), 3'ss of exon 1
----------------------------ggtggtgttggttttttttttttttttgggtgggggggggggaattgtgacgatctgagtgttggtgacggtggatctgtggcgtt--tttgtgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGT
| |||| || | | | || | || | | | |||||| || | ||| | | || || ||||||||||| ||| |||||||||||||||| | |||||||||| | || | | ||||||||||||||||||| |||||||| ||||| ||||||||||
gtgagtgccgcgccccgtcgcctcctcacgcttcgttgcttgcaatcaacgcgatcgtctggtctcgtcttgttccagtgtgtcatttctctctgacgggtgagatttggtttggatctggtcggaccagGTGCTCCACGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCACATCTCCACCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGT
upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044027_T01 (Zea mays), 3'ss of exon 1
ggtggtgttggttttttttttttttttgggtgggggggggggaat-tgtgacgatctgagtgttggtgacggtggatctgtggcgtttttgtgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGT
| | | | || | || | | ||| ||||| | | |||||| | | || | | || ||| |||||| |||| ||| |||||||||||||||| |||||||||||| | || | | | ||||||||||||||||||| || ||||| ||||| ||||||||||
gtgagcgccgcgcccttcgcccccctcaggccctcacgcttcgttgcttgatcgtctga-tttctctgacgggtgttttggtttggatctgggcggaccagGCGCTCCACGCGATGGCGCAGAAGGAGACCAATGGCAGCAACGGCGAGCACATCTCCACCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTMapped 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|88738635|gb|CI762143.1|CI762143EST: TCCAAGCTTGCTCTCCTCTNNNNNNNAATCCTTCCCTCCCGAGTGGCAGG GTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAG
genomic: TCCAAGCTTGCTCTCCTCTCCCCCCCAATCCTTCCCTCCCGAGTGGCAGGgtgagcattc ... tgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAG
EST:
gi|88400725|gb|CI596146.1|CI596146EST: TCCAAGCTTGCTCTCCTCTNNNNNNNAATCCTTCCCTCCCGAGTGGCAGG GTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAG
genomic: TCCAAGCTTGCTCTCCTCTCCCCCCCAATCCTTCCCTCCCGAGTGGCAGGgtgagcattc ... tgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgacgatctgagtgttggtgacggtggatctgtggcgtttttgtgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGT
tttttgt CT-rich tract
tttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtggtgttggttttttttttttttttgggtgggggggggggaattgtgacgatctgagtgttggtgacggtggatctgtggcgtttttgtgcgtaccagGTGCTCGACGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGT
ggtggtg
- - - - - - - - - - - - - - - - - - - - - - -tgtgacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggatc