Sequence
atgc intronic sequence ATGC exonic sequencegtacgcacaaattcaatgtggtaaaaatatttcctcagagtttggttaaaattgtaagatgaatgctcacttcagGTGTACAACATGGTCAAGGCCTTCAAGGAGAAGAGGCCGAAAGAGCAGAGCCAAGTACCATCGAGGAAAAGGAGTAGACGGCTGAAGTAGCAAATCTTCA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g10910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g10910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G425986_T02 (Zea mays), 3'ss of exon 6
gta-cgcacaaattcaatgtggtaaaaatat----ttcctcagagtttggttaaaattgtaagatgaatgctcacttcagGTGTACAACATGGTCAAGGCCTTCAAGGAGAAGAG----GCCGAAA--GAGCAGAGCCAAGTACCATCGAGGAAAAGGAGTAGACGGCTGAAGTAGCAAATCTTCA
||| | | ||| | | | | | ||| || | | | | || |||| | ||| |||| ||||||||||||||||||| ||| ||||||||||| || || | | ||| | || ||||| |||||||||||| ||||||| | ||| | |
gtaactcccaactgaagcatttatacagtatcaagttgcattaaactgaatcaagattgatacgtgagc-ctcaaaacagGTGTACAACATGGTCAGGGCTTTCAAGGAGAAAAGCCTCGCTGTATCTGAGATAGGTCATGTACCCACGAGGAAAAGGACTAGACGGTTAAAGCGGTAGC------Mapped 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|112785459|gb|EE590735.1|EE590735EST: TTGACGAAAATGCAGTCGACTCAATAGGATTGATATCAGGGATCCGGAAG GTGTACAACATGGTCAACGCCTTCAAG-AGAAGAGGCCGAAAGAGCAGAGC
genomic: TTGACGAAAATGCAGTCGACTCAATAGGATTGATATCAGGGATCCGGAAGgtacgcacaa ... ctcacttcagGTGTACAACATGGTCAAGGCCTTCAAGGAGAAGAGGCCGAAAGAGCAGAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaaaatatttcctcagagtttggttaaaattgtaagatgaatgctcacttcagGTGTACAACATGGTCAAGGCCTTCAAGGAGAAGAGGCCGAAAGAGCAGAGCCAAGTACCATCGAGGAAAAGGAGTAGACGGCTGAAGTAGCAAATCTTCA
tgctcac putative branch site (score: 2)
ctcacttc CT-rich tract
ttaaaattgtaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcacaaattcaatgtggtaaaaatatttcctcagagtttggttaaaattgtaagatgaatgctcacttcagGTGTACAACATGGTCAAGGCCTTCAAGGAGAAGAGGCCGAAAGAGCAGAGCCAAGTACCATCGAGGAAAAGGAGTAGACGGCTGAAGTAGCAAATCTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG