Sequence
atgc intronic sequence ATGC exonic sequence...catatcctaatctgatgttttggaccatcttcgatgaagtggaattcttgtttgttttttcttgttaagaatttatcttataagctttatttttgaacagTTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAAGAAAGGTAATGCCAGCTGGAATAATTGCTGCCGTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g38790.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g38790.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G895534_T01 (Zea mays), 3'ss of exon 1
catatcctaatctgatgttttggaccatctt-cgatgaagtggaattcttgtttgttttttcttgttaag--aatttatcttataagctttatttttgaacagTTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAAGAAAGGTAATGCCAGCTGGAATAATTGCTGCCGTCAG
|| | | || | | | || | || | | ||| ||| | | | || | | | || | | |||||| ||| | || ||||| ||||||||||||||| ||| ||||| || ||||||||||||||| |||||||| |||| ||||||| |||||||| | ||| | ||||
-at-ttgtgatttcctatccaggtctatgatgtgtcaaagctctattgtgttaggcttggtatccatcagttagtatatcttctaa-ccttgttttttaacagTTTGTGCTGTGCTATTGACTGTTGTCATGGGAATAAGATACGTCAAAACACAAAAGATAATGCCTGCTGGAATTGTCGCTTCTATCAGMapped 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|88475499|gb|CI412770.1|CI412770EST: CGCGCGCGGCCACCCCAGCGGCTCCCTCTTCGCCGCCGTCCTCCAGACTG TTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAA
genomic: CGCGCGCGGCCACCCCAGCGGCTCCCTCTTCGCCGCCGTCCTCCAGACTGgtccgtttct ... ttttgaacagTTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAA
EST:
gi|88963034|gb|CI025520.1|CI025520EST: CGCGCGCGGCCACCCCAGCGGCTCCCTCTTCGCCGCCGTCCTCCAGACTG TTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAA
genomic: CGCGCGCGGCCACCCCAGCGGCTCCCTCTTCGCCGCCGTCCTCCAGACTGgtccgtttct ... ttttgaacagTTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtttgttttttcttgttaagaatttatcttataagctttatttttgaacagTTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAAGAAAGGTAATGCCAGCTGGAATAATTGCTGCCGTCAG
ctttattttt CT-rich tract
ttaagaatttatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatcctaatctgatgttttggaccatcttcgatgaagtggaattcttgtttgttttttcttgttaagaatttatcttataagctttatttttgaacagTTTGTGCTGTAGCATTAACTGTCGTTATGGGAATAAGATACATCAAAACAAGAAAGGTAATGCCAGCTGGAATAATTGCTGCCGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC