Sequence
atgc intronic sequence ATGC exonic sequenceGGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttcttctcgatccgatccattttcgtggccacattgcggtttttttttatttgcgtgtgagacggtgagcatgccgctgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g37837.3 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g37837.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G172101_T01 (Zea mays), 5'ss of exon 2
GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttct-tctcga--tccgatccattt------tcgtggccacattgcggttttt--ttttatttgcgtgtgagacggtgagcatgccgctgtgcag
|||| |||||||| ||||| |||||||||||||||||| ||||||||| | || ||||||||||| || ||||||||| |||||| | |||| || | | | || | | |||| | |||| | || || || | | || || || |||||
GGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCCgtacgttctgtctcgaattgcgatgcactcatcatcccttttccttctcggggttctgggttttgtgtgagtatgtgttcggtggcgtgtttctttgcag
upper sequence: LOC_Os01g37837.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G014367_T02 (Zea mays), 5'ss of exon 2
GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttct-tctcgatccgatccattttcgtggccacattgcggtttt----tttttatttgcgtgtgagacggtg-agcatgccgctgtgcag
|||| |||||||| || || |||||||||||||||||| ||||||||| | |||| ||||||||| ||||||||||| ||| || | |||| | | || | | || | || | |||||| || || || || |||||
GGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGACAAGCTCAAAGCTgtacgttccgtctagaattgtgaagcgctcgtcatccctttttcttctcggggttctgggtttcatgtgagtgactgtggcgtgtttctttgcag
upper sequence: LOC_Os01g37837.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124439_T01 (Zea mays), 5'ss of exon 2
GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttct-tctcgatccgatccattttcgtggccacattgcggtttt----tttttatttgcgtgtgagacggtg-agcatgccgctgtgcag
|||| |||||||| || || |||||||||||||| ||| ||||||||| | |||||||||||||| || |||||||| ||| || | |||| ||| || | | || | || | |||||| || || || | | |||
GGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTTAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCCgtacgttccgtctagaattgcgaagcgctcgtcatcactttttcttctcggggttctgggtttcatgtgagtgactgtggcgtgtttttttacag
upper sequence: LOC_Os01g37837.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G014367_T01 (Zea mays), 5'ss of exon 2
GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttct-tctcgatccgatccattttcgtggccacattgcggtttt----tttttatttgcgtgtgagacggtg-agcatgccgctgtgcag-----
|||| |||||||| || || |||||||||||||||||| ||||||||| | |||| ||||||||| ||||||||||| ||| || | |||| | | || | | || | || | |||||| || || || || |||||
GGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGACAAGCTCAAAGCTgtacgttccgtctagaattgtgaagcgctcgtcatccctttttcttctcggggttctgggtttcatgtgagtgactgtggcgtgtttctttgcagagcaa
upper sequence: LOC_Os01g37837.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G355297_T01 (Zea mays), 5'ss of exon 2
GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttct-tctcgatccgatccattttcgtggccacattgcggtttt----tttttatttgcgtgtgagacggtg-agcatgccgctgtgcag
|||| |||||||| || || |||||||||||||||||| ||||||||| | |||||||||||||| || ||||| | ||| || | || | ||| || | | |||| || | |||||| || || || || |||||
GGCAGTTCGAGCTAGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCCATACGTACCgtctagaattgcgaagcgctcatcatcactttttcttctcggggttttgggtttcatgtgagtgactgtggcgtgtttctttgcagMapped 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|29633861|gb|CB638870.1|CB638870EST: TCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT AAAAAGGAGGACGCGTCGGCTCTGATTCAGAGCACGGAAGAGATTAAGAAG
genomic: TCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttctt ... cgctgtgcagAAAAAGGAGGACGCGTCGGCTCTGATTCAGAGCACGGAAGAGATTAAGAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCAATTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCTgtacgttcttctcgatccgatccattttcgtggccacattgcggtttttttttatttgcgtgtgagacggtgagcatgccgctgtgcag
- - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA