Sequence
atgc intronic sequence ATGC exonic sequencegcaagtgttttttcgctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55410.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 9
----------------------------gcaagtgttttttcgctattagaaatgaattatctctagtc----cagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
| | ||||| |||||| ||| || ||||| || |||||||| || ||| |||| ||||||||||| || ||||| |||||||| || || ||||| || ||||||||||| ||||| || || ||||||||||| ||||| || |||| ||| || |||
tagtttaagtaattcgacactattgtacatgaattattttttgctatttaaaactaaaggtctctggttggttcagtgacactaa--tgtgcatttcaacagTTCCTAAAATTTGTAGAGAAGACTGCACCTATTGCAGTATATACATCTGGCAAAGGATCGTCTGCAGCTGGTCTTACAGCATCTGTAACTCGTGATAGTA
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 9
----------------------------------gcaagtgttttttcgctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
||| |||||| ||||| ||| || ||||| || ||||| || || || || |||||||||||||| ||||| |||||||| || || ||||| |||||||||||||| ||||||||||| ||||||||||| ||||| || |||| |||||| |||
taagtcagtttgagtattttgacactattgtacaacaatcattttttt-ctatttaaaaccaag-gtctctggttcagtggcactaa--tgcgtgtttcaacagTTCCTCAAATTTGTAGAGAAGACTGCCCCTATTGCAGTCTATACATCTGGCAAAGGTTCATCTGCAGCTGGTCTTACAGCATCTGTAACTCGGGATAGTA
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------------------------------------------gcaagtgttttttcgctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
|| | | | ||| || | || | | | | ||| |||| ||| | | || |||||| || |||||||| || ||||| || || |||||||| ||||| ||||| ||||| |||||||||||||| || || || || ||||| | || |
gttagttttatgtgtatatatattttgccagaccaattttttaattaatttgtggcaattgagttgttaaaaacctattgggccactgccattttcattttttcgttcacattgtagcttgttttctcctgtgagttgaccattaccttttttacagTTTCTGAAGTTTGTTGAAAAGACTGCCCCTATTGCTGTTTATACTTCTGGAAAAGGCTCATCAGCAGCTGGCCTAACCGCTTCTGTAATCCAAGATAGCG
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------gcaagtgttttttc--gctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
| ||||| |||| | | | | | | | | || | | | | | | | | | |||| || ||||||||||||||||| || || |||||||| ||||||||||| || |||||||| || ||||| |||||||| || || ||||| || | |
ttcaagtgttagattacaatccttacaaaatgtctgtgttatttccaacacctgtagcttacatgtttaaagcttaattgctt---attttttttctctctagTTTCTTAAGTTTGTGGAGAAGACGGCTCCAATTGCTGTTTATACATCTGGAAAGGGTTCATCGGCTGCTGGGCTCACAGCTTCGGTGATTCGAGATAGCA
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------gcaagtgttt---tttcgctattagaaatgaattatctctagtccagtgacatgaaac-----tgtacattcca--------acagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
| || | | | | | | | | | | || || || | || ||| ||| ||| | |||||||| || ||||| |||||||| || ||||||||||| ||||| ||||| || || || ||||| ||||| || || || || || ||||| ||| ||
tttagttcccttcagtaaagttctgggtccgtcgactgggatggcaatagctgtacataatacccacgaaggatgtgtgtgtattgccttggctatgcagTTCCTAAAATTTGTTGAGAAGACTGCACCGATTGCTGTTTATACCTCTGGAAAGGGCTCCTCAGCTGCTGGGCTTACTGCATCCGTTATTCGTGACTCTA
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ17142 (Selaginella moellendorffii), 3'ss of exon 9
gcaagtgttttttcgctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
|| || | | | | || || | || | | | || | ||||| | || ||||||||||| || |||||||||||||| ||||||||||| || ||||| || || ||||| | || || || || || || || | |
-----------------gttggatttcagt-gctttggttcttgtttctctaatgttttccttgta-cagTTTTTGAAATTTGTGGAGAAAACTGCGCCGATTGCTGTGTATACATCTGGCAAGGGTTCCTCTGCTGCTGGATTGACTGCATCCGTCATACGTGATGCGA
upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ31205 (Selaginella moellendorffii), 3'ss of exon 9
gcaagtgttttttcgctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
|| || ||| | | ||| || | || | | | || | ||||| | || ||||||||||| || |||||||||||||| ||||||||||| || ||||| || || ||||| | || || || || || || || | |
-----------------gttggatttgagt-gctttgggtcttgtttctctaatgttttccttgta-cagTTTTTGAAATTTGTGGAGAAAACTGCGCCGATTGCTGTGTATACATCTGGCAAGGGTTCCTCTGCTGCTGGATTGACTGCATCCGTCATACGTGATGCGAMapped 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|58671106|gb|CK059792.1|CK059792EST: GGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG TTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGG
genomic: GGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAGgcaagtgttt ... attccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGG
EST:
gi|58679471|gb|CK068158.1|CK068158EST: GGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAG TTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGG
genomic: GGGACATTCATGTCTTGCTGCTGGGTGATCCATCAACAGCAAAATCACAGgcaagtgttt ... attccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
aaatgaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtgttttttcgctattagaaatgaattatctctagtccagtgacatgaaactgtacattccaacagTTCCTCAAGTTTGTGGAGAAGACAGCGCCGATTGCTGTCTATACATCTGGGAAAGGTTCATCAGCAGCTGGTCTCACAGCGTCAGTAATTCGGGACGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG