Sequence
atgc intronic sequence ATGC exonic sequenceATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaagttgcaatgtatcatcagagacttctgcattttcaatctgcggtcattgtgttcattgaaaggaaatacaatagccacctagactaatttgttaaag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g02020.2 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g02020.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM5G860137_T02 (Zea mays), 5'ss of exon 12
ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatg--cagttatttgttgtactgattattcatgtatagttttgtgtaagttgcaatgtatcatcagagacttctgcattttcaatctgcggtcattgtgttcattgaaaggaaatacaatagccacctagactaatttgttaaag
||||||||||| ||||||||||| |||| |||||||||||||||||||| || || || ||||| ||||| ||| |||| |||||||||| | || | | ||| || ||| | | | | ||||| |||| ||||| | | | ||||| | | | | | ||| |
ATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctcttcactttttttttgttcctcaaacttttttcccctgcaaaaggaaattttcagttctctatgatactg-----ttccatctgatcgtcagtaggac----------------------------------------------------------------------------------------------
upper sequence: LOC_Os01g02020.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S160_44V6.2 (Physcomitrella patens), 5'ss of exon 12
--------------ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtg-taagttgcaatgtatcatcagagacttctgcattttcaatctgcggtcattgtgttcattgaaaggaaatacaatagccacctagactaatttgttaaag
|||| | | |||||||| | ||||||| ||||| || || ||||||||||| ||||| ||||| |||| ||||| |||||||||| ||||| | ||| || || ||| | | | | | |||||| | | | | || | | | || | || ||||||
TCACACTGCTCGGGGTTCTGAAGGAGAAAAATGGTCACTTTGGGGTCGCTGGTGTGTGTAATGGAGGTGGAGGTGCATCTGCTGTTGTGGTGGAGCTCATgtaag----------gtttgca-tggtctaaccatttcccagatt----agccattcccttccactgttgtggtaactgcaaaggtgttgatacgtaatttcttacaatgttctc-----------------------------------------------------------------------------------
upper sequence: LOC_Os01g02020.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S160_44V6.1 (Physcomitrella patens), 5'ss of exon 12
---------ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaagttgcaatgtatcatcagagacttctgcattttcaatctgcggtcattgtgttcattgaaaggaaatacaatagccacctagactaatttgttaaag
|||| | | |||||||| | ||||||| ||||| || || ||||||||||| ||||| ||||| |||| ||||| |||||||||| | || | | | || | | | | || | || || | || | | | || || || ||| | || | | | ||
CTGCTCGGGGTTCTGAAGGAGAAAAATGGTCACTTTGGGGTCGCTGGTGTGTGTAATGGAGGTGGAGGTGCATCTGCTGTTGTGGTGGAGCTCATGTAAGgtttgcatg-gtctaaccatttcccagattagcc-attcccttccactgttgtggtaa----ctgcaaaggt-gttgatacgtaatttcttacaatgttctcttcat-------------------------------------------------------------------------------------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|15008105|gb|AU222493.1|AU222493EST: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT TATCTGACTTGATGCAGGCAACCATCACTATTTACACGTTCCTCGTTGTGA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... tttgttaaagTATCTGACTTGATGCAGGCAACCATCACTATTTACACGTTCCTCGTTGTGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaagttgcaatgtatcatcagagacttctgcattttcaatctgcggtcattgtgttcattgaaaggaaatacaatagccacctagactaatttgttaaag
- - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG