Sequence
atgc intronic sequence ATGC exonic sequence...aagaaaatgcattgcaatctccatcatggttaaatattgtgtttgctaattgcttggtgttgataatgcacttatgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g20420.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 7
aagaaaatgcattg-caatc-tccatcatggttaaatattgt-gtttgctaattgcttggtgttgataatgcacttatgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG
| || ||| |||| | ||| | ||| | | || | ||||| || | | | | || | || || || | ||| || | ||| ||| | | ||| || ||||| || |||| | |||||||||| ||||| ||||||||||| |||||| |||||||||
gtaagcatagtttgacaataatgcattctagttcactcttctagtttgtatgcaactcaa--ctaaca-tctgggagtgttatttttcattacattgcattagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G30150.1 (Glycine max), 3'ss of exon 7
aagaaaatgcattgcaatctccatcatggttaaatattgtgtttgctaattgcttggtgttgataatgcacttatgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG
|| || | | | || || | |||| |||| | || | ||||| || || ||| |||||| ||||| ||||||||| || || ||||| |||||| || || ||||||| |||||||||||||| || |||||||||||||| ||
ttttaattgttgtatgcttttttgttccattccattgttaatttgttaatcataaaatattttcttggaccttatatattgtgtttacactttggcatagGTGGGTGTTATGTTGAAGGAAATTATCTAAGAAATGCATTTAGGTGGAAAGACACGGTTGGACCCTGGGAAGAGAGACCAGGGCACTTTAATGATGTATG
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 6
---aagaaaatgcattgcaatctccatcatggttaaatattgtgtttgctaattgcttggtgttgataatgcactta-tgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG
| | | || |||| || | | | | || | || | | | | | ||| |||| ||| || | |||| |||||| | ||| ||| | ||| || ||||| ||||||| || | ||||||| |||||||||||||||||||||||| |||||||||
atgatccatcttttttccaatttcttcctcgaatttgtctttatgtcatcaagcgttcaa-ataacttccaaatttaatgca---attttttatctttcaagagGTGGCTGTTTTGTTGAAGGACAAACATTAAGAAATGCATTTCGGTGGAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTGMapped 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|157650374|gb|EX450008.1|EX450008EST: TCTTGCCACTATGCTGGCAAATCTGAAGCCTCGGTTTTTAAAATTTCCAG GTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTG
genomic: TCTTGCCACTATGCTGGCAAATCTGAAGCCTCGGTTTTTAAAATTTCCAGgtttgtcatc ... ttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTG
EST:
gi|33658179|gb|CF280793.1|CF280793EST: CTTGCCACTATGCTGGCAAATCTNGAAGCCTCGGTTTTTAAAATTTCCAG GTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGGAGT
genomic: CTTGCCACTATGCTGGCAAATCT-GAAGCCTCGGTTTTTAAAATTTCCAGgtttgtcatc ... ttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGG-AGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaattgcttggtgttgataatgcacttatgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG
tatgtttctttttttt CT-rich tract
atatgtttcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaaaatgcattgcaatctccatcatggttaaatattgtgtttgctaattgcttggtgttgataatgcacttatgcatatgtttcttttttttctgcagGTGGAAACTATGTCATGGGAAATTATTTACTGAACGCATTCCGGTGGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA