Sequence
atgc intronic sequence ATGC exonic sequencegtacctatttattcttagaacatttgcatcttgctgactttttgaagtgggaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g46510.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 17
-----gtacctatttattcttagaacatttgcatcttgctgactttttgaagtgggaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
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gtattttgattactttttttctccctctttccataatcattgctttttaattcagatatcggtattctcacattatactttttctaa----cagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA19G41130.2 (Glycine max), 3'ss of exon 13
-----gtacctatttattcttagaacatttgcatcttgctgactttttgaag-tgggaaatgcaaatg-----gtgtaatattcaaaaactaatgtg---cagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
|| || || ||| ||| | |||| | | | | | ||| || || || || ||| | | || |||||| | ||||||||| | || || |||||||| | || || |||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||
gtattgtgattactttctctccctggttttccctctttttccataatcattgcttattaattcagatatgtctgtatatctctcattatactttttgaaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 3'ss of exon 17
gtacctatttattcttagaacatttgcatcttgctgactttttgaagtgg--gaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
||| || | || | | | | | | ||| | || |||| | | ||| | | | || ||| | || ||||||| | ||| ||||| | || |||||||| || ||||| ||||||||||| || ||||| || || || ||||| |||||||| ||||||||||| |||
gtatggatatgtttctcataatctcgtgtttatgtgagtagtt-aagtagctggaatcc---ttatacaacattt-----tttttgcgcagGGCAAGTAGGCTTGGGAGAGAACATCATGACGATCTGGCACAGTTTATGCTAGGGATGGGATACGCAACAGAAGCTCTTCATTTGCCTGGAATATCTAAG
upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv08s0056g00040.t01 (Vitis vinifera), 3'ss of exon 21
gtacctatttattcttagaacatttgcatcttgctgactttttgaagtgggaa-atgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
||||| || || ||||| ||||| |||| | | | ||| | | | | || | | | |||||||| | ||| |||| | |||||||||||||| | ||||| |||||||| |||||||| ||||| ||||||||||||||||| ||||||||||| |||
----gtattttttttttttccattt-----ttgcttgctttctcgtgcataatcatgtttcta-tacacaaaataacaccatttatgcagGGCTAGTAGGCTTGCAAGAGAGCATCATGATGATTTAGCTCAATTTATGCTTGGAATGGGTTATGCCACTGAAGCACTTCATTTGCCTGGAATATCTAAG
upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ13686 (Selaginella moellendorffii), 3'ss of exon 17
gtacctatttattcttagaacatttgcatcttgctgactttttgaagtgggaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
| |||| || | | | ||| | | |||||||| || ||||| || ||||| ||||| ||||| ||||| |||||||| || ||||| |||||||||||||| | ||| | || || || || |||
--------------------------------gtacgtttttctgcatgatagtacttactttaccggcattttatg-----tttgcagGGCTTTCAGGCTTGGACGAGAGCACCATGACGACCTTGCTCAATTTATGCTAGGCATGGGATATGCTACTGAAGCTTTACATCTGCCGGGCATTTCGAAGMapped 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|58671972|gb|CK060658.1|CK060658EST: AGATGTCGGTGCCTTGCAGCATATGGAGATCCAGTTAGTGCCGTGAAATG GGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCT
genomic: AGATGTCGGTGCCTTGCAGCATATGGAGATCCAGTTAGTGCCGTGAAATGgtacctattt ... taatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCT
EST:
gi|58655020|gb|CK043700.1|CK043700EST: AGATGTCGGTGCCTTGCAGCATATGGAGATCCAGTTAGTGCCGTGAAATG GGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCT
genomic: AGATGTCGGTGCCTTGCAGCATATGGAGATCCAGTTAGTGCCGTGAAATGgtacctattt ... taatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgactttttgaagtgggaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
aactaat putative branch site (score: 2)
taatattcaaaaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctatttattcttagaacatttgcatcttgctgactttttgaagtgggaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC