Sequence
atgc intronic sequence ATGC exonic sequence...tctacactagagggcacatagacaatatcataatgttccattataatctgtctgaatttgaggtgtgcatacatttggtgtattaatttgcttattgcagAGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCGGTGTGGTGCTGCTAGAGCTGGCCACCGGCCGAGGGCCGCAAGATGGTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g13430.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g13430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100234_T01 (Zea mays), 3'ss of exon 1
tctacactagagggcacatagacaatatcataatgttccattataatctgtctgaatttgaggtgtgcatacatttggtgtattaatttg-----cttattgcagAGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCGGTGTGGTGCTGCTAGAGCTGGCCACCGGCCGAGGGCCGCAAGATGGTGG
| | || | | || || || | || || |||| | | | | | | | || | ||||||||| ||| ||||| |||| ||||||||||| ||||||||||| ||||||||||| ||||| |||| || | ||||| || || || ||
-------------gtgatttgattactctgttgcgtc---ttgtacgcaaaaaaaaaaagacacgtgcgtgc-ctggacggcctgacctgagagtttggctgcagAGTATTTTAGCAGAGTGAAGGTGAGCGAGAAGGTGGACGTCTACAGCTTCGGGGTGGTGCTGCTGGAGCTCACCACAGGAAGGGGGCCACAGGACGGCGG
upper sequence: LOC_Os02g13430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G176206_T01 (Zea mays), 3'ss of exon 1
------tctacactagagggcacatagacaatatcataatgttccattataatctgtct--gaatttgaggtgtgcatacatt-tggtgtattaatttgcttat-------tgcagAGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCGGTGTGGTGCTGCTAGAGCTGGCCACCGGCCGAGGGCCGCAAGATGGTGG
||| | | | || || | | || || | ||| || ||| || ||| | || || | | || || ||||||||||| | | | | ||||| | | ||||| ||||| ||||||||||| ||||||||||| |||||||| ||||| | | | | || | |
gtgcgttcttaatcggccgtgcggcagtcaccagc-cggccaacccttctggtcttctcaggaggctgaaatgaatcgacactctgctgatctgctatggttggaattggatgcagAGTACGGACGCGGCGCCAAGGTGAACCAGAAGGTAGACGTGTACAGCTTCGGCGTGGTGCTGCTGGAGCTGGCGACCGGGAGGGTAGCCAACGACAGCAGMapped 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|88205180|gb|CI205029.1|CI205029EST: CGTCTGTGGCACCTTTGGCTACATTGCTCCAG AGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCG
genomic: CGTCTGTGGCACCTTTGGCTACATTGCTCCAGgtatctacta ... cttattgcagAGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgtctgaatttgaggtgtgcatacatttggtgtattaatttgcttattgcagAGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCGGTGTGGTGCTGCTAGAGCTGGCCACCGGCCGAGGGCCGCAAGATGGTGG
tattaat putative branch site (score: 2)
tttgctt CT-rich tract
tattaatttgcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctacactagagggcacatagacaatatcataatgttccattataatctgtctgaatttgaggtgtgcatacatttggtgtattaatttgcttattgcagAGTACGCATACAGGTCAAAGGTAAGCGTTAAGGTGGACGTATACAGCTTCGGTGTGGTGCTGCTAGAGCTGGCCACCGGCCGAGGGCCGCAAGATGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - -gcacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttggtg