Sequence
atgc intronic sequence ATGC exonic sequence...aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08400.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------aataattg-acatgtgaaagttgttaaca-tgtgttaagtaaca-gccgacaatttctttttgtttttttaaatgcgccatcttac--------agttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
| ||| | | ||| | | || | | || || || | | ||||| | || | ||| |||| | || |||||| |||||||||||||||||||||||||||| ||||||||||| ||||||||||||||| |||||||||||||||| |||||||| |||| |||||||| || ||||
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttctt-ttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttctt-----attcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
|| | | || |||| | | | || || | | | || || || | | || | |||| || | | || || |||||||| || ||||| |||||| ||||| ||||||||||||||||||||| ||||||||| |||||||| ||||||| || |||||||| | || |
-tcctttttgaattacaaattgtccgc-tttattttgtt-ctttcaatt-ttgctagttatagatataca-gcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 6
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttcttattca-----gATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
| || || | || ||| || | | || || | | | ||||| || | | |||| | | || | || || || |||| |||||| ||||| ||| || ||||| ||||||||||||||||||||| |||||||||| |||||||| |||||| || |||||||| | || |
-cttttttgaatttagaa-ttgcccac-tttattttgtt-ctttcaattttttctagttatagatataaa-gtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
aataattgacatgtgaaagtt--gttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatc-ttacagttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
|| | | || ||| | | | || ||| | | | | || || | | | | ||| | | ||| | |||| || || ||| |||||| ||||| |||||||| |||||||||||| ||||||||||||| |||||||||||| | || || ||| | | || |
---tcttcatgaacagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttcttattca-----gATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
|| | | | |||| || | | || || | | || ||||| || | | |||| | | || | || || || |||| |||||| ||||| ||| || ||||| ||||||||||||||||||||| |||||||||| |||||||| |||||| || |||||||| | || |
--ccttttttgaattagaattgtccac-tttattttgtt-ctttcaactttttctagttatagatataaa-gtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G38640.3 (Glycine max), 3'ss of exon 3
aataattgacatgtgaaagtt---gttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatc-ttacagttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
|| | | ||| | ||| | | | || | | | | || || | | | | ||| | | ||| | |||| || || ||| ||| || ||||| |||||||| |||||||||||| ||||||||||||| |||||||||||| | || || ||||| | || |
----cttcatagaacaaaccttaagtttgccttttcaaaaaagaaaaaaatggcagtaagatacattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGTCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTCCTCGTTGTT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatg----cgccatcttacagt-------tccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
||| | ||| || ||||| | ||| | | ||| | | |||| ||||| | ||| || ||| | || | |||||||| ||||| ||| | || ||||||||||||||||||||| | ||| | |||||||| ||||||||| || || ||||| | || |
---------cattttgaagaaactag-atgtgcaatgta-tatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 7
aataattgacatgtgaaagttgt-taacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacag--ttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
|| || || || ||| || | | || || | | ||| | | | || || || |||||| || | |||||||| |||||| ||| || ||||| |||||||||||||| |||||| | ||||| |||||||| ||||| ||| || || ||||| | || |
--tattttgaataaactagatgtgcaatgtatattt-gtttcttttgtatgtttttcacaaatgatactgtagcatcaatgtatttctttcctttttgtacagATTCCAACAAATGCAGCTGGACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTTMapped 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|56158549|gb|AU095148.2|AU095148EST: CATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT ATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGG
genomic: CATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcg ... tcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacaatttctttttgtttttttaaatgcgccatcttacagttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
atcttac putative branch site (score: 3)
ttccttcttattc putative PPT
tttctttttgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatgcgccatcttacagttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG