Sequence
atgc intronic sequence ATGC exonic sequencegttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04190.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 10
-------------gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
| ||| | || | |||||| | || | | |||| ||| || ||| ||||||| |||||||| ||| | | || |||||||| ||||| |||||||| |||||| |||||||| | |||||||| |||||||| ||||||||||||||||| ||| || |||||||||| ||||||||||
gttgtgatacgttgacatgacagttgctttgttcaaaacctaatgctgttgtgatatgtacttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtact-----ctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG
upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 6
---------------------------------------gttgtgataac-tgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
| || | ||| | | | || | | ||||||| |||||| | || |||||| ||||||| ||| || | ||| ||||||| ||||| |||||||| |||||| |||||||||| |||||||| |||||||||||||||||||||||||| ||| || |||||||||| ||| ||||||
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaatgctacagttacttctgtctttgttcaatagctactgcatgcattgacgaacatctccaacaaatgaact---tgtactt-----tgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 6
gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
| | | || | || || || | | | ||| | || ||| | || | || | | ||| |||||||||||| |||||||| ||||| || || || ||||||||||| |||||||| |||||||| |||||| || ||||| ||||| | ||||||||||
---------------gtgctttatatattattcttatctttgag--atcatagactaaataatt---tatgtggactg--tgtggtaactcctctta-atgggcagATTTCACCAACTGAAATTCGTGGTGCGCTAGGATCTGTTAATCAACTTTTTATATGCATTGGGATTCTTCTGGCACTGGTGGCTGGGCTGCCTCTGGCAG
upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G16150.3 (Arabidopsis thaliana), 3'ss of exon 5
gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
||||| || | ||| ||| || || | ||| | | | ||| || | | ||| |||| ||| || | ||||| ||||| |||||||| ||||||||||| || ||||| || ||| | || ||||| || ||||| ||||| || || ||||||||||||| || ||||
gttgtttaaat--actgattttcattatttttgcactt--ttagc-ataagatgttagatttgtttatatgttatgtctctgaagcgtttgatgatg-gttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG
upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 6
gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttct-tgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
|| ||| ||||| || | || ||| || |||| | | | | | || | |||| | |||||| | | || ||||| ||||| |||||||| ||||| || ||||| ||||| ||||| |||||||| || ||||| |||||||| || |||| |||||||||||||| ||
---gtagtaat-----gtttcaatttttcattattattattatgctattttttgttcgtttttatgaatgcctttga-aactgaaacacat---tttaaatggtcagATCTCACCAACTGAAATTCGTGGTGCGCTTGGGTCTGTCAATCAACTTTTTATTTGTATTGGGATTCTTGCAGCATTGGTGGCTGGATTACCTCTAGCCAMapped 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|66924477|gb|CX111325.1|CX111325EST: GGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG ATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTT
genomic: GGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAGgttgtgataa ... gcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTT
EST:
gi|300215629|gb|HO088255.1|HO088255EST: GGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAG ATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTT
genomic: GGATTGGTATTGGCATATCTTCTGCTCTTGTGCCCCTTTACATATCTGAGgttgtgataa ... gcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
tattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA