Sequence
atgc intronic sequence ATGC exonic sequenceCGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgcatttatcagtaaaaaaaggcaattcgtgataaatcacttgtctgtaaacttggtaatccagttgacagtttacctacg...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g41870.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G057618_T01 (Zea mays), 5'ss of exon 4
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgcatttatcagtaaaaaaaggcaattcgtgataaatcacttgtc--tgtaaacttggtaatccagttgacagtttacctacg
|||||||||||||||||||||||| ||||||||||||| || |||||||| |||| || ||||||||||||||| |||| ||||| |||||||| ||||||||||| |||||| | ||| || | | ||| | | | | ||||| || || | || || | || ||| |
CGAAATGTTGTAATGCTGATTGGTTTTTGTGTTGAGGACAGAAGGCGTTTATTGGTTTACGAGTACATCTGCAATAGATCTTTGGACTCACATCTCTATGgtaagattgttttctcggtagcacttttgtacatgaaaccattagtttggttgtggtacttgctgtctccaagttcatgatgcacctaact-tttgtgttt-
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G480607_T02 (Zea mays), 5'ss of exon 5
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgcatttatcagtaaaaaaaggcaattcg-tgataaatcac-ttgtctgtaaacttggtaatccagttgacagtttacctacg
|||||||||||||||||||| ||| |||| |||||||| || |||||||| |||| || ||||||||||||||| |||| |||||||||||||| |||||||||| | |||||| | | |||||| | ||| | || | | || || ||||| | || || | || || || ||| || ||
CGAAATGTTGTAATGCTGATAGGTTTTTGCGTTGAGGACAGAAGGCGTTTATTGGTTTACGAGTACATCTGCAATAGATCTTTGGATTCACATCTCTATGgtaagaccgttttctcggtaggatttatgtacataaaccattagtttggtcatggcacatgctgtct-tcaagttcttgatgcacttaacaactt-tgtatt
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G20750.1 (Glycine max), 5'ss of exon 4
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgcatttatcagtaaaaaaaggcaattcgtgataaatca-cttgtctgtaaacttggtaatccagttgacagtttacctacg
|| |||||||| ||||| ||||| | ||| | ||||||| || | | ||||| |||||||| || ||||||||||| |||||||||||| | |||||| | | | | | | || | | | | ||| | ||| | || || | | || | || | | | | | |
CGCAATGTTGTTATGCTCATTGGGTTCTGTATAGAGGATAAAAGAAGGCTACTGGTTTATGAGTATATATGCAATGGATCATTGGATTCACATTTATATGgtgattttttctggctcccataccaaattatctcatgatagaaatatatttagaattggcctgaacttagtgaagattgtcaaattcataatctgtcaaa-
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G03340.2 (Glycine max), 5'ss of exon 3
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttg---catttatcagtaaaa--aaaggcaattcgtgataaatcacttgtctgtaaacttggtaatccagttgacagtttacctacg
|| |||||||| ||| | ||||| ||||||| |||||| | ||| | ||||| || |||||||||||||||||||| || ||||||| ||| | || |||| || ||| | |||| ||| || || | | | | | || | || || | | || || | | | |
CGCAATGTTGTGATGTTAATTGGGTTTTGTGTGGAGGATGGAAGGAGATTGCTAGTTTATGAGTACATCTGCAATGGCTCTCTGGATTCTCATATCTACAgtaaattcctttgaatccttgatttttttttcgctacattcataaccggctgtggagacttctgttcttcttttcatttctagctttacccatactacat-----
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G01350.1 (Glycine max), 5'ss of exon 4
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgc--atttatcagtaaaaaaaggcaattcgtgataaatcacttgtctgtaaacttggtaatccagttgacagtttacctacg
|| |||||||| ||||| ||||| | ||| | ||||||| ||| | | ||||| |||||||| || ||||||||||| |||||||||||| | |||||| | || || || | | | | ||||| | | | || | | | | || | | || || | | || |||| | | | | | |
CGGAATGTTGTTATGCTCATTGGGTTCTGTATAGAGGATAAGAGAAGGCTACTGGTTTATGAGTATATATGCAATGGATCATTGGATTCACATTTATATGgtgatttctcttgctcccataccaaattatc--tcatgatagaaatatatttagaattggcctgaacttagtgaagattttcaagttcataatctgtcaagt
upper sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 5'ss of exon 4
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgcatttatcagtaaaaaaaggcaattcgtgataaatcacttgtctgtaaacttggtaatccagttgacagtttacctacg--------
|| |||||||| ||||| || || | ||||| |||||| | || | |||||||| ||||| || ||||||||||| || |||||||| |||||||||||||| || | ||| || || |||| || | || | || | |||| | || | | ||| || | | || | |
CGCAATGTTGTGATGCTAATCGGGTTCTGTGTGGAGGATGGAAGAAGGTTGCTGGTTTATGAATATATCTGCAATGGGTCTTTGGATTCCCATCTTTATGgtaa-attgtcttcattttt-----tatccacaatataat-tattttatagtaaaat-catggcaatgtgcttatgaaactgactcccaagcagtcactgctttctttMapped 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|25798254|gb|CA754215.1|CA754215EST: GCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATG GTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTG
genomic: GCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcat ... taaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGAAATGTTGTAATGCTGATTGGTCTTTGTGTTGAGGATAGGAGGCGTTTGCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcattttctttcttgcatttatcagtaaaaaaaggcaattcgtgataaatcacttgtctgtaaacttggtaatccagttgacagtttacctacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa