Sequence
atgc intronic sequence ATGC exonic sequence...aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttgttaaaatcttttaaatgatatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g04990.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
---aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttg-ttaaaatcttttaaatgatatatatga-------attgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
| ||| | || | | | || | | || | || | | | ||| ||| ||| || || || | || | | || || |||||||||||||||||||||||||| |||| |||| | || |||||||||||| | ||||| ||||||| | |
gtaagcagctccattgtcaacctatgacactttctgggcct-tcttcgttttttcattcaaatttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 4
---aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttg-ttaaaatcttttaaatgatatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
| ||| | || | | | || | | | || || || | | | ||| ||| ||| || || ||| | | | || || ||||||||||| |||||||||||||| |||| |||| | || |||||||||||| | ||||| |||||||| |
gtaagcagctcaattgtcaacctatgacactttctgtgcct-tctttgttttttcattcaaatttacttagcatccttctcat--tattccttcactttttaagGTACAAATGGATAACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATCATGGAATCGAAAAG
upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttgttaaaatcttttaaatga-tatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
|| | | | | | || || | | | | || | | || | |||| | | | ||| ||| | | | | || || ||||||||||||||||||||||||||||||| ||||| | ||||| ||||||||||| | || | || ||||| ||
gtgagctcctaacttactcaatctatgtgtatctgcaagaaagtactttcctt-gaagct------agttttcttatgtgactctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 4
aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttgttaaaatcttttaaatgatatatatgaattgt-----tgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
|| | | | | || | | | | | | || | | || | || | || ||| || | || | || || |||||||||||||||||||||||||| | || |||| || ||||||||||||||| | | ||||| || |||
gtaagctagctatcacttatgaactttgtatttcaagttgattcagtggcagatagttctccactgaagttgcttgaattggttacttttcttctacacttgaagGTACAAATGGATGACATATGGAGAAGCAGGCACTGTCCGGTTGGCAATAGGTTCTGGTCTTCGTCATCATGGGTTATTAGAA
upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 4
aacagttggggagtaagaattggtt-cctggatatatatgtcattattgccttttgtagctttgttaaaatcttttaaatgatatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
||||| ||| | ||| ||| | || || || ||| || | ||| || ||| || | | | | || || |||||||||||||||||||||||||| |||| || | || || ||||||||| | || ||| |||||||||| ||
------------gtaag--ttgctcatctgaataactttgctat--ttcatcattgaagttccctta--ttcatttgcattcattgcctacact-ttcaagGTACAAATGGATGACATATGGAGAAGCAGGTACTGCTCGATCAGCAATTGGTTCTGGTTTAATATACTATGGAATACCGAAAMapped 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|33675569|gb|CF303808.1|CF303808EST: AATAGATTCCCTGATAACCCAGACATTGGAACGCTTCATGATAACTTTGT CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGG
genomic: AATAGATTCCCTGATAACCCAGACATTGGAACGCTTCATGATAACTTTGTgtaagaatcc ... attgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgccttttgtagctttgttaaaatcttttaaatgatatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
tttgttaaaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttgttaaaatcttttaaatgatatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - gttcctg