Sequence
atgc intronic sequence ATGC exonic sequence...tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 3'ss of exon 8
-tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccacaatgttgaggtgttctt------attttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
||||| || | || | || || | | |||| ||| | | || | || | |||| ||||||| || | || | |||| ||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||| || |||||
ctggaaaatgttcta--tactgatttctgaacgcc----acttgtgttgctctttataatctca-tcctgagatgttctttgttttatatcttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 7
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccacaatgttgaggtgttctt-attttttaattta------ttttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
|||| || | |||| || | | | | | |||| ||| || ||| | |||||||||| |||| || ||| |||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||| ||||||||
----atatcctatactggttg--agtccgagtgctgcttgtgttactctttataatt-tcataatcctaaggtgttctttgttttatactttgaactatttttgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 7
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccaca-atgttgaggtgttctt------attttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
|||| || | || | | || | | |||| ||| | | || | || || |||| ||||||| || | || | |||| ||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||| || |||||
-ggaaaatgttcta--tactaatttctgaacgcc----acttgtgttgctctttataatctcatatcctgagatgttctttgttttatatcttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatg-attgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
| || ||| | || | | || || | | | | | | || ||| | || || | | || | | | | | ||| || ||||||||||| | ||||||||||||||| |||| |||||| ||||||| ||||||||||| | |
ttacatgtttttaagatttcaccaaaat-tagtttgaaattgagattatggatatattccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
tggaatatttgttagttgttggcagctcactactt-aatacttatgtcag-ttatgattg---ccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
| ||| || || | | || || | | ||| | || ||||| | | || || | | || | || | | | ||| || ||||||||||| | |||||| |||||||| |||| |||||| |||||||| ||||||||||| | |
-----tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccacaatgttgaggtgttcttattttttaatttatt----ttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
||||| | ||| ||| | | | ||||| | |||| | | | || | | || ||| | | || | | ||| || ||||||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| |||| | |
----ctattttatttccgtttacagtttttaagctgatactaaatgtagttggaagtatattttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 8
tggaatatttgttagttgttggcag-ctcactacttaatac-ttatgtcagttatg-attgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
| | ||| | || |||| | | | | | || | ||| || ||| | | | || | | |||| || ||||| || | || ||||||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| |||| | |
tttacagtttttaagctgttactaaatttagttggaagtatactttgtaagatatatactaattctccattttaat--ttttatggttcaatttgctt-gcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
tggaatatttgttagt-tgttggcagctcactacttaatacttatgtc-agttatgattgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
| ||| ||| | | || || | | | | || | | ||||||| | | | | || | || | || | | || || ||||||||| | || |||||||||||| |||| |||||||||||||||||||| |||||| | |
--tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCGMapped 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|58609972|gb|CK038005.1|CK038005EST: ACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAG ACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATA
genomic: ACTGGATCTGAAGATGGCACAGTTCGCATATGGCATTCGACAACTTACAGgttgctttca ... tattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagttatgattgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
ttttaat putative branch site (score: 3)
tttatttt CT-rich tract
tgttcttattttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatgattgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG