Sequence
atgc intronic sequence ATGC exonic sequence...aatgaggttcccctatgcatacatattcgttataaccttctgcattaatatagaggatcttgatttaagtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g41590.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 2
aatgaggttcccctatgcatacatattcgt-tataaccttctgcattaatatagaggatcttg-atttaagtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
| | || ||| | | || || | | | | | || || | ||| ||| | || | | ||||| || |||||||||||| || || || ||||||||||||||||||||||| || ||||||||||||||||| || ||||||||||||||||| ||||| |||||
agcaaaatttgtacgc-tatatcgggtagcgcattacatccagtgcct-cacggtcagcctaatatatgtaccatattgctgaacatggtcttatcgtgcagGTATGGTGGCGGCCCTTACGAATGAGAGTGCAACCAGCAAATCAGTATACTTTTCACTTTGCACATCGGAAATGATATACATCACTCATCTTCTAGCACC
upper sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 2
-aatgaggttcccctatgcatac-atattcgttataaccttctgcattaatatagaggatcttgattta--agtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
| | | || ||| || | | | || | | | || | | | | || || | || |||| || | | |||| || ||| ||||| ||||| || |||||||||||||| || |||||||| || |||||| ||| |||||||| |||||||||| ||||| ||| | | || ||
gtttaacatacctctaattttatgagaggcattcccatgtcttacacttgatttctgatttacaatctataaatcctgtttttcattttaatgttgtc----agGAATGGTAGCTGCCCTTACCAATGAGAGTGCTACAAGCAAATCTGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCATTTGTTGGCTGA
upper sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
---aatgaggttcc-----cctatgcatacatattcgttataaccttctgcattaatatagaggatcttgatttaagtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
|| | ||||| ||| | | | | | | || | | ||| || || | || || ||| || |||| || | | || | || ||| ||||| || || || || ||||||||||| || |||||||| || |||||| ||| |||||||| |||||||||| ||||| || | | || ||
aagaaaggggttcaacatacctctacttttagaggcattcccatgtcttgctttctgatttataat----atataaatcctgtttttcattttaatgctgtc----agGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
upper sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
aatgaggttcccctatgcatacatattcgttataaccttctgcattaatatagaggatcttgatttaagtcatgttgttaaataccttg---ttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
|| || | || | ||| |||| || | ||||| ||| ||| | || | | ||| | ||| ||| || | ||| ||||| || || ||||||||||||||||| ||||||||||| || |||||| ||| ||| || || || ||||| | || |||||||| || | ||
-gcattcttgtgtgatcctgttctaatttatatttccttttg-aagaatattgagtttctgggttggaatt-tgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGAMapped 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|58608296|gb|CK036329.1|CK036329EST: CACTCATGAAGTAATGGGCGGCTTAAAGAACATATATGCCATTGGTGCTG GTATGGTGGCTGC
genomic: CACTCATGAAGTAATGGGCGGCTTAAAGAACATATATGCCATTGGTGCTGgtaagttcca ... tatcttgtagGTATGGTGGCTGC
EST:
gi|4714589|gb|AU055706.1|AU055706EST: CACTCATGAAGTAATGGGCGGCTTAAAGAACATATATGCCATTGGTGCTG GTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACT
genomic: CACTCATGAAGTAATGGGCGGCTTAAAGAACATATATGCCATTGGTGCTGgtaagttcca ... tatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatagaggatcttgatttaagtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
ccttgtt CT-rich tract
ttgttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaggttcccctatgcatacatattcgttataaccttctgcattaatatagaggatcttgatttaagtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
- - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - - cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttg