Sequence
atgc intronic sequence ATGC exonic sequencegtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
--gtaatcaaatcatctgcatttcttttc-cattttaatttcg---tatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
|| ||| | || ||||||||| | | ||| | | ||| || | || | | | ||| || | | | ||||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||| |||||
gtatactcatctatacttcatttctttctgtacagaagttttagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 7
-----------------gtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatt-tagaacttcctcatcctt----ttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
|||| ||| || ||||| || ||| || | || | ||||||| |||||| | || | | |||| || | ||| |||||||||||||| ||||| |||||||||||||| |||||||||||||| |||||||| |||||||| |||||
gtacttatacttatttaaacttcaacagttcttcacttcttcctgatcttagtt-cataggtacataaattctagaacactgtgatacatatcatttttttttgctgtgcattagATATCTTGTCCTTGCCAATATGTTGATGGAGTCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 7
--gtaatcaaatcatctgcatttcttttc-----cattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
| || | | || | || || || | | | | | | ||| | | || | || || | | | | || || |||||||| || || ||||||||||| |||||||| ||||| ||||||||||| |||||||||||
ctgagatttagcatttagcttgactatttggaaacaaaccattcaagcaaccttttttcttttgtatttaacttgtaacatagtttctatttcgtgtcagGTACCTTGTTCTGGCCAACATGTTGATGGAGTCTGAAGTAAATCCTTTTGATGGGCAGGAGGCTAAGCC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
gtaatcaaatcatctgcattt---cttttccattttaatttcgtatattgata-aatttagaacttcctcatccttttttattgt----actgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
| | | | |||||| ||| | |||| || | ||| | || | || | | | | | || || | | ||| | || || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| |||||||||||
-tttcctgagatttagcatttaagcttgactatttgaaaataaaccattcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 7
gtaatcaaatcatctgcatttctt--ttccattttaatttcgtatattgataaatttagaacttcctcatcctttt---ttattgtactgcata--ttagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
| |||||| | ||| || | | || ||| | || || | | | || |||| | | | ||||| | || | || || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| || ||||||||
aaatccaaatcccttacatatcatgacttcaaaataaaccattgaatacatcattctttgcttttgacatcttgtacaataattgttatttatgagtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGGCAGGAAGCTAAGCC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
gtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcct----catcctttt---ttattgtactgcata--ttagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
||| ||| | || || | |||| | | || | ||| | | | | |||| | | | ||||| | || | ||||| ||||||||||| || ||||||||||| |||||||| ||||| |||||||| || || ||||||||
gtag--gaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgcttttgacatcttgtacaataattgttatttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 7
----gtaatcaaatcatc----tgcatttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
| || || | | || | |||| | | | | | || | || | | | | ||||| || || | || ||||||||||| || |||||| ||||||| || ||||||||||| |||||||| |||||||| |||||
gagcattattcgattactcttgtccagtaactttctgtgatcggtccaaacatgttagagttaatgatctttgttttttttttcttttggctatgcaa-agGTATCTTGTTCTGGCGAATATGCTGATGGAGTCAGAAGTGAATCCGTTTGATGGCCAAGAGGCAAAGCCMapped 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|55827482|gb|AU032236.2|AU032236EST: TTCAAAAACTATGATGAAGCTTGCAATCCGCGGGGAATTCAATGCCTGAA ATATCTTGTTCTTGCAA-TATGTTG
genomic: TTCAAAAACTATGATGAAGCTGGCAATCCGCGGAGAATTCAATGCCTGAAgtaatcaaat ... tgcatattagATATCTTGTTCTTGCAAATATGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
tattgat putative branch site (score: 3)
attgataaatttagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcctcatccttttttattgtactgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG