Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacataacctttgtacctcatttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g07110.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 9
gtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacataacctttgtacctcatttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
||||| ||| | ||||||||| ||| || | |||| | | | | | | ||||| ||| | | ||| | | ||| ||| ||| |||||||||||| || |||||||||||||||||||||||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| || ||||| ||||
gtatggtgttctcctaccaatatattcatagattgtttcaggcattgaact--ttaacttcttcacactttctgtaacaataaccacacaccacatatattatgtgaagGATGATGAGAAAGGTATGCGATGGTTCTATTCTGGAGACATCGGACGGTTCCATCCAGATGGCTGCCTTGAAATCATTGACCGTAAGAAAGATATCGTGA
upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G03280.1 (Glycine max), 3'ss of exon 8
gtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacat--aacctttgtacctcat--ttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
|| || | | | | | || | | | | | | | || | | || || ||| ||| | | || | |||||||| ||| |||| ||| ||| | ||||| || |||||||||| ||| | | || |||||||| ||||||||||||||||| ||||||||||| ||||| |
-------------ttgtcagtttttgtgtttttatttttattttatgtggggggaggagagaagctaaaaaggtacaaattaaatgtttttactttgtactttttctgtgaagGTTGATGAAAGAGGAATGAGGTGGTTTTACACTGGTGACATTGGGAGAGTTCATCCAGATGGATGCCTTGAAATCATTGATCGTAAAAAGGACATTGTTA
upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA14G23710.1 (Glycine max), 3'ss of exon 10
gtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacataacctttgtacctcatttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
|||| ||||| | | | || | || || | | | | | | || |||||| || | | ||| | ||||||| ||| |||| || ||| | ||||| || | |||||||| ||| | | || |||||||| ||||||||||||||||| |||||||||| ||||| |
-----ttgt-ttgtt-ttattttatttatt--ttattttatgtggagggaggagagaaggtaaaaaggtacaaattacatgtttttactttttacttttttccgtgaagGTTGATGAAAGGGGAATGAGGTGGTTTTACACCGGTGACATTGGGAGAGTGCATCCAGATGGATGCCTTGAAATCATTGATAGTAAAAAGGACATTGTTAMapped 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|29622299|gb|CB627310.1|CB627310EST: TTCAAGAATGAAGCTAAAACAAATGAAGTCTATAAG GATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTC
genomic: TTCAAGAATGAAGCTAAAACAAATGAAGTCTATAAGgtatgttgtc ... tcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccttctatccacaataatttacataacctttgtacctcatttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
tttatctt CT-rich tract
acaataatttacataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgtcttgttaccaatatgttcgatgactacttcacggctcatagtaataaccttctatccacaataatttacataacctttgtacctcatttatcttgtgaagGATGACGAAAAAGGTATGCGATGGTTCTATTCTGGTGACATCGGGCGCTTCCACCCAGATGGCTGCCTTGAAATCATTGACCGTAAAAAGGATATTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG