Sequence
atgc intronic sequence ATGC exonic sequenceCCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgcttcaacttattctcctcggacaaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 2
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgcttcaacttattctcctcggacaaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca---
|||||||||||||||||| |||||||||||||| || |||||||||||||| ||||| ||||| || || |||||||| | |||||||| || || ||||| |||| | | | | | | ||| | | | | | || |||| | | | || || || |||| | |
CCAGAAGAAGATGGCCGGTCGCGCGCTGCTCCTTGCGGGCCCGCCCGCCACGGGCAAAACGGCGCTAGCGCTCGGCATAGCGCAGGAGCTCGGCAGCAAGgtccgtgcgcctagtggcttatatttgttttctggtact-tcgaagaaatgattttattgcttcg--ccatttttctctgttgtgggtcacatgagtggagcc
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G018697_T03 (Zea mays), 5'ss of exon 3
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgc-ttcaa---cttattctcctcggac---aaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca
||||||||||||||||||||| ||||||| || || ||||||||||| ||||||||||| || || |||||||| | |||||||| || || ||||| |||| ||| || ||| | ||||| | | || |||| |||||| || | || | |||| |||| || | ||
----AAGAAGATGGCCGGCCGCGCGGTGCTCCTTGCGGGTCCGCCCGCCACGGGCAAGACGGCGCTAGCGCTCGGCATAGCCCAGGAGCTCGGCAGCAAGgtccgtgcgttcggttgctcatttttctcggtcctcacacgaagcagctgttcattcatttgg--tggtaaagggaggggtttatttctcc--cccaaggtcct---
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G018697_T02 (Zea mays), 5'ss of exon 2
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgc-ttcaa---cttattctcctcggac---aaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca
||||||||||||||||||||||||| ||||||| || || ||||||||||| ||||||||||| || || |||||||| | |||||||| || || ||||| |||| ||| || ||| | ||||| | | || |||| |||||| || | || | |||| |||| || | ||
CCAGAAGAAGATGGCCGGCCGCGCGGTGCTCCTTGCGGGTCCGCCCGCCACGGGCAAGACGGCGCTAGCGCTCGGCATAGCCCAGGAGCTCGGCAGCAAGgtccgtgcgttcggttgctcatttttctcggtcctcacacgaagcagctgttcattcatttgg--tggtaaagggaggggtttatttctcc--cccaaggtcct---
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 2
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgcttcaacttattctcctcggacaaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca
|||||||||||||||||||| || || || |||||||| ||||||| |||||||||||||| | || || || || |||||||| || | |||||| | |||| | |||| | ||| |||||| | | | | | | ||| | | | | || |
GCAGAAGAAGATGGCCGGCCGGGCACTTCTTCTCGCCGGACCGCCCGGGACCGGCAAGACGGCATTGGCACTTGGAATAAGCCAGGAGCTTGGCACCAAGgtttctttctcaa--gactctcattctttgtgttgtg--attgttaccccttcttgctgcttataattaagtttattccactctgcag------------
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 2
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgcttcaacttattctcctcggacaaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca------
|||||||||||||||||||| || || || |||||||| || |||| |||||||||||||| | ||||| || || |||||||| || | |||||| |||| | |||| | | || || | || ||| ||||| || | || | ||| | | | |||| ||
GCAGAAGAAGATGGCCGGCCGGGCACTTCTTCTCGCCGGACCACCCGGAACCGGCAAGACGGCGTTAGCTCTTGGGATAAGCCAGGAGCTTGGCACCAAGgtttccctctcaa--gactctcattctcgtggtgttttttttttctctgtgttttgattg-tgacccttcttgct-gctgataataatgtttatgccactctgcag
upper sequence: LOC_Os01g62040.3 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 3
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgt--------tggtgcttcaacttat--tctcctcggacaaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca
||||||||||||||||||||||| || ||||||||||| | || | || || ||||| || || ||||| || || | ||||| || ||||||||||| || | |||||| | | | | | | | | | | | | || ||| |||| | || ||| || | || |
GCAGAAGAAGATGGCCGGCCGCGCACTTCTCCTCGCCGGGGCTCCTGGAACGGGGAAGACTGCTCTGGCTCTTGGAATTGCCCAGGAACTCGGTAGTAAGgtaacggcaatgcttcttcaattgaaaacgtgtcaaggctcatgtcaatgctcctacgagttctgcatttatggg---atattagaacttttggagcacatat-------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|33676655|gb|CF304894.1|CF304894EST: CCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAG GTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAG
genomic: CCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgctt ... cataacacagGTCCCCTTCTGTCCTATGGTGGGATCAGAAGTGTATTCCTCAGAGGTCAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCAGAAGAAGATGGCCGGCCGCGCGCTGCTCCTCGCCGGCCCGCCCGCCACCGGCAAGACGGCCCTCGCTCTCGGCATCTCTCAGGAGCTAGGTAGTAAGgttggtgcttcaacttattctcctcggacaaactgtattattgttggggtatttggattgatggagataaatgtttgcttctgaaatgcacaatgctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT