Sequence
atgc intronic sequence ATGC exonic sequenceATAAATGTGAAGACTAAGGTTGTGTCTGGGTCACCTCCTGGTGTTGTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAAgtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g41870.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G480607_T06 (Zea mays), 5'ss of exon 3
ATAAATGTGAAGACTAAGGTTGTGTCTGGGTCACCTCCTGGTGTTGTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAAgtaagggtcaaatcctattacagtg--tgcataaatacatcataaccttttttttttctgttttct-----tatgtttcatgtttctgctaattag------
|||||||||| | |||| |||| || || || ||| ||||||||||||||||||||| |||| |||||| ||||||||||||||| |||||||||| || |||| | ||| |||| | | | |||||||| || | ||| || | |||| || ||| ||||| ||||| |
ATAAATGTGAGGTATAAGCTTGTTTCCGGCTCTCCTTCTGGTGTTGTAGCTGCTGAGTGCAAGCAAGCACAGGCAAGCTGGGTTGTGCTAGACAAgtatgg-tcaactgctaaatcagtagtttcttgaatacatcctacgttctttcattgttatttttgcttaataaattttatgttgctgctgctgctgctcag
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G057618_T02 (Zea mays), 5'ss of exon 4
ATAAATGTGAAGACTAAGGTTGTGTCTGGGTCACCTCCTGGTGTTGTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAAgtaagggtcaaatcctatt-------acagtg----tgcataaatacatcataaccttttttttttctgttttct-----tatgtttcatgtttctgctaattag-
|||||||| | | |||| |||| || || || ||| |||||||||| |||||||||| ||||| |||||||||||||||||||||| ||||||||||| |||||| || | ||||| | | |||||| | || | ||| || | |||| || || ||||| ||||| ||
ATAAATGTAATGTATAAGCTTGTTTCCGGCTCTCCTTCTGGTGTTGTTGCTGCTGAGTGTAAGCAAGCACAAGCAAGCTGGGTTGTGCTAGACAAgtaatggtcaactctcaactcctgaaacagtagttttttttgaatacagcctacattctttcattgttatttttgcttaataaattgtatgttgctgctgctttagMapped 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|112785737|gb|EE591308.1|EE591308EST: GTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAA GGAGTTGAAGCATGAAGAGAAACATTGCTTGGAGGAGCTACAGTGTAATAT
genomic: GTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAAgtaagggtca ... tgctaattagGGAGTTGAAGCATGAAGAGAAACATTGCGTGGAGGAGCTACAGTGTAATAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATAAATGTGAAGACTAAGGTTGTGTCTGGGTCACCTCCTGGTGTTGTAGCTGCTGAGTCTAAGCGAGCACAAGCAAGCTGGGTTGTGATAGACAAgtaagggtcaaatcctattacagtgtgcataaatacatcataaccttttttttttctgttttcttatgtttcatgtttctgctaattag
- - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG