Sequence
atgc intronic sequence ATGC exonic sequenceGAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatatatatatatatatatatatatttgacatcagcaaaaaccatatgcaacattaagttcacgatatacatacttagcatccatgaaatgccaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g33940.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G104074_T01 (Zea mays), 5'ss of exon 3
GAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatatatatatatatatatatatatttgacatcagcaaaaaccatatgcaacattaagttcacgatatacatacttagcatccatgaaatgccaa
|||||||| || ||||| ||||||||||||| ||||| |||||||| || ||||||||||||||||||||||| || |||| ||||| || | |||||| | || | | | || | || | | | | ||| | | | | | | || | ||| | | |||
AAAGACCCTGGTGTTCTATATCGGCAGGGCGCCGCACGGGAAGAAGACTGAGTGGATCATGCACGAGTACCGCCTTGATGAAGAGAACGTTGAAATTCAGgtaacaagctagaggccttgtgttgtacacttc-tttaatttgtttctactagcagctggcaagttgtaaagca-actctgatgatc--taatctgcag-
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G041746_T01 (Zea mays), 5'ss of exon 3
GAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatatatatatatatatatatatatt-tgacat----cagcaaaaaccatatgcaacattaa-----gttcacgatatacatacttagcatccatgaaatgccaa------------------
||||||||| || |||||| ||||||||||||| |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| || | |||||| ||| | | ||||||||||| ||| | | | ||| ||| | | || | | |||| | | || | | | | | ||
GAAGACCCTGGTGTTCTACATCGGCAGGGCGCCACACGGCAAGAAGACTGACTGGATCATGCACGAGTACCGCCTGGACCAAGAGAACGTTGAGATTCAGgtaataataaaggggcctttatatatatatcctgatctagtcctgtaaataccgttctttattttgtttcttgctagcgatcgagctgctgcaatgcaaagtgactcaaatcctgatatggtctacag
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G041746_T02 (Zea mays), 5'ss of exon 3
GAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatatatatatatatatatatatatt-tgacat----cagcaaaaaccatatgcaacattaa-----gttcacgatatacatacttagcatccatgaaatgccaa---------
||||||||| || |||||| ||||||||||||| |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| || | |||||| ||| | | ||||||||||| ||| | | | ||| ||| | | || | | |||| | | || | | | | | ||
GAAGACCCTGGTGTTCTACATCGGCAGGGCGCCACACGGCAAGAAGACTGACTGGATCATGCACGAGTACCGCCTGGACCAAGAGAACGTTGAGATTCAGgtaataataaaggggcctttatatatatatcctgatctagtcctgtaaataccgttctttattttgtttcttgctagcgatcgagctgctgcaatgcaaagtgactcaaatcctgatat
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 5'ss of exon 2
GAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCA-Ggtatatatatatatatatatatatatatatttgacatcagcaaaaaccatatgcaacattaagttcacgatatac------atacttagcatccatgaaatgccaa---
|| |||||| ||| ||||||| || ||| ||||||||||||||||||||||||||| ||| || ||| | | |||| | ||| ||| | || || | | | | || | || | || | || | || | | | | | | | || || || || |
---------GGTGTTCTACAAGGGCCGGGCGCCTCATGGCCAGAAGACCGACTGGATCATGCACGAGTTCCGTCTAGACGACGGCAACCAGGCATTCCGCGGTTTCGATgtacgtcgccgt-tccacatttccaaccccctcacagtgttcgtgtccctttcgatcagtgttgcattaccagaaagcttgcctcggagatgctcccagat
upper sequence: LOC_Os06g33940.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ22020 (Selaginella moellendorffii), 5'ss of exon 2
GAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatatatatatatatatatatatatttgacatcagcaaaaaccatatgcaacattaagttcacgatatacatacttagcatccatgaaatgccaa
|||||| || || || || |||| ||||||||||||||||||||||||||||| | ||||| | |||| | | | | || || | || || ||| || | | | | | ||| || | | || | ||||||||
------------TTTCTACAGAGGGAGAGCTCCAAACGGGCAGAAGACCGACTGGATCATGCACGAGTACAGGCTCGAGGAGGACATCAGCAGCAGTGGCAGCAACAACAATgta-agatcctctcgtacttggca---------gcttttttcttctataaccctcttatttttttggttt-tggctctgaaatgcag-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|88377590|gb|CI605425.1|CI605425EST: ACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAG GAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGA
genomic: ACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatat ... atcattgcagGAAGATGGTTGGGTGGTGTGTAGGGTATTCATGAAGAAGAGCTACCAGCGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAGACCCTCGTCTTCTACGTCGGCAGGGCGCCCCACGGCAAGAAGACCGACTGGATCATGCACGAGTACCGCCTCGACCAAGACAACGTCGATGTCCAGgtatatatatatatatatatatatatatatttgacatcagcaaaaaccatatgcaacattaagttcacgatatacatacttagcatccatgaaatgccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcaaaaa