Sequence
atgc intronic sequence ATGC exonic sequence...gttggtgatgtttcaacttgtcattgttaatattcaatttgaggcacactatgattcttgctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g06454.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g06454.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G040587_T01 (Zea mays), 3'ss of exon 3
gttggtgatgtttcaacttgtcattgttaatattcaatttgaggcacactatgattctt----gctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT
|| | | |||||| || | || || | | | | | | || | | || || || | ||| | | |||||| ||||| |||| || | | | |||||||| |||||||| ||||| | ||| ||||| ||||| ||||| ||||| || || |||||||||||||| || ||||||
----gtactagtgtggtcagtcattcttgagtttttataagtgtcgctgcttagtgattaaacgtttttttttcatgctagcttataattattgatgtttccagGGAAACTGCCAACGCAGAGAAGGTAAAAGAGGCGCACAAGAGGGTTATGGTCGCCAACCATCCAGATGCTGGTGGAAGTCATTACCTTGCGTCAAAGATT
upper sequence: LOC_Os01g06454.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0040g02370.t01 (Vitis vinifera), 3'ss of exon 2
gttggtgatgtttcaacttgtca--ttgtta-atattcaatttgaggcacactatgattcttgctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT
| | || | | ||| || || || || | ||| || | ||| ||||| || ||| | | |||||| | || ||| |||| | | || ||||| || || ||||| | ||||| |||||||| ||||| || |||||||| ||||| ||||||||||| || || |||
ccaaaccacactccacttcccaagtttgatatattttttccttaattcaccctgt-atttcacctattatttattaatttattttttaaacttttga--acagGGAAAGCACTCCAGCAGATAAGGTCAAGGAAGCACATAGGAAGGTGATGGTTGCAAATCACCCTGATGCAGGTGGCAGCCATTACCTTGCCTCAAAAATT
upper sequence: LOC_Os01g06454.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
--gttggtgatgtttcaacttgtcattgttaatattcaatttgaggc-acactatgattcttgctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT
| || | ||| ||| | | ||| | || | | | | ||||| |||| || ||| || || || || |||| | | || ||||| || || ||||| | | ||||||||| || || ||||| |||||||| || ||||||||||||||||| || ||
caactaatgcc-tgtcattttgaagtcat--gtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATCMapped 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|88410630|gb|CI686967.1|CI686967EST: TTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAG AGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGT
genomic: TTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAGgtacatatca ... atgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactatgattcttgctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT
ttttgat putative branch site (score: 4)
tctcttttttcttttg CT-rich tract
ttttttcttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgatgtttcaacttgtcattgttaatattcaatttgaggcacactatgattcttgctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
gttggtg
- - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - ggcacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttgc