Sequence
atgc intronic sequence ATGC exonic sequencegtgcatactgttttgatctaaacttctactgttattgttttcttctctaatattttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g16290.2 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 16
-gtgcatactgttttgatctaaacttctactgttattgttt--tcttctctaatattttct--ttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
||||| || | ||| ||| || | | || ||| |||| || ||||| || | || |||| ||||||||||| ||||| ||||| || |||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||||| ||||||||||
gttgcattctttcttgttctcttattatgatttttccctttgctcttatcaaatatattatactttagGGTGAGGATTTTAAGAAGGAGGCTCTCCGGTATCATAAGATAGTTATACTTACTGACGCTGATGTTGATGGAGCACATATCCGGACTCTCCTCCTTACTT
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA19G31030.1 (Glycine max), 3'ss of exon 16
---------------------------------gtgc-atactgttttgatctaaacttctactgttattgttttcttc---tctaatattttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
|||| | | | |||| ||| |||| | ||| | | | | | || |||||||| ||||||||||| || || || || |||||||||||||| | || | |||||||||||||| |||||||| || ||||| || || || || || |
caattatatcagagtaaaaatccttgatcacctgtgccagaatcctttgctcttaactaacataaaaattttaattaggaaattccttttgttgtttcagGGAGAGGATTTTAAGAAAGATGCACTCCGATATCATAAGATTATTATTTTGACTGATGCTGATGTGGATGGTGCCCACATCCGAACACTGCTACTGACAT
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 16
-------------------------gtgc-atactgttttgatctaaact----tctactgtt--attgttttcttctctaatattttct-----ttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
|||| | | |||| ||| |||| | ||| || || ||| || ||| | || | ||||||| ||||||||||| ||||| || || |||||||||||||| | || | |||||||||||||| |||||||| |||||||| ||| | || || || |
tcagagtaaaaatccttgataacctgtgctggaatcctttgctcttaactaacataaactatttgatattttaattaagaaatgtcttttgttgtttcagGGAGAGGATTTTAAAAAGGATGCACTCCGATATCATAAGATTATTATTTTGACTGATGCTGATGTGGATGGTGCCCATATCCGAACTTTGCTACTGACAT
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G04130.1 (Arabidopsis thaliana), 3'ss of exon 16
----------------------------------gtgcatactgttttgatctaaacttctactgttattgttttcttctctaatattttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
| | | |||| | | | || || | | |||| || |||||||| || |||||||| || ||| | | || || ||||||||| |||| | || ||||| ||||| |||||||||||||||||||| ||||| | || |
gtgatgtatccattttccatctcttgtttttccttttctctttttttttttttgggtgtata-tggaaaactcaatgcaataaataacttgtttcagGGAGAAGATTTTAAGAAAGAAAATTTGCGGTACCATAAGATAATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G10270.1 (Arabidopsis thaliana), 3'ss of exon 17
---gtgcatactgttttg-atctaaacttctactgttattgttt-----tcttctctaatat----tttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
| || || ||| ||| | | || ||| | | | | || || |||||||| || |||||||||||||| ||| || || ||||| || |||| | || ||||| ||||| |||||||||||||||||||| ||||| | || |
gtaatatatcctttttcatatcctgctgtttgttggtatgttcggaaaactcagtttgacataaaacttatttcagGGAGAAGATTTTAACAAGGAGAATCTGCGTTACCATAAAATTATCATCTTAACAGATGCAGATGTTGATGGTGCACATATCCGGACACTTCTGTTGACCT
upper sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 16
----------------gtgcatactgttttgatctaaacttctactgttattgtttt------------cttctctaatattttc--tttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
| | || ||||| | | |||| | ||||| || ||| | || || |||||||| ||||||||||| ||||||||||| || |||||||| || |||| | || ||||||||||| |||||||| |||||||| ||||| || | ||||
gttaactcattttttgttccttaggtttttgtttttgttttctttttttatttttggtgaacagtacagcttattctatcttcctggtttcagGGGGAGGATTTTAAAAAGGAAGCTCTCCGTTATCATAAAATCATCATCTTAACAGATGCTGATGTGGATGGTGCTCATATCCGAACTCTGCTGTTGACTTMapped 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|58689240|gb|CK077927.1|CK077927EST: AAAACGAAGAGATCCAAAATCTAATTGTCGCTCTTGGATTAGGAGTAAAG GGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTC
genomic: AAAACGAAGAGATCCAAAATCTAATTGTCGCTCTTGGATTAGGAGTAAAGgtgcatactg ... tttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttgatctaaacttctactgttattgttttcttctctaatattttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
ctctaat putative branch site (score: 3)
ttgttttcttctctaa CT-rich tract
tctaatattttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcatactgttttgatctaaacttctactgttattgttttcttctctaatattttctttcagGGCGAGGATTTTAACAAGGAAGCTCTTCGATATCATAAGATAGTCATACTCACTGATGCTGATGTAGATGGTGCACATATCCGGACTCTTCTCCTTACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT