Sequence
atgc intronic sequence ATGC exonic sequencegtattaacatttctaaatgagctttttggacatttaaattgaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g34620.8 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g34620.9 (Oryza sativa), 3'ss of exon 3
lower sequence: AC208327.4_FGT002 (Zea mays), 3'ss of exon 4
gtattaacatttctaaatgagctttttggacatttaaatt-------gaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
||||| |||| | ||||| || | | ||||| ||| |||| || || |||||| ||| |||||||| | | || || |||||||| | | || || || | | ||| || |||||||||||||||||||||||||| |||||||||||||||||| |||||| |||| | |||||| |||||||| |||| |||| ||| | |||||||||
gtatttacatgcggagatgagattcaagaatatttatattaaacattgaagcacctaacttgtggtaaaactaggcataacctgaatcttattgatgtatctttttagcttcc--attctttcataccattttttggcagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTTCAGCAATATG
upper sequence: LOC_Os01g34620.9 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 3
gtattaacatttctaaatgagctttttggacatttaaatt-------gaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
||||| |||| | ||||| || | | ||||| ||| |||| || || ||||| ||| |||||||| | | ||| || |||||||| | | | || | || | | | || | || ||||||||||||||||||||||| |||||||||||||||||| |||||| |||| | |||||| |||||||| |||| |||| ||| || |||||||||
gtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaagcttattgatgtatcttt-ttagctgccatctcttcttatcattttcttggtagGATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGMapped 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|58675402|gb|CK064089.1|CK064089EST: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
tgttaat putative branch site (score: 3)
atttgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaacatttctaaatgagctttttggacatttaaattgaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA