Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g19700.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcatt-catatt-tgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatag----atagaaatattgaatcttatatgatttatgat----tcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
||| || ||| | || || | | |||| | | | || || | | | |||| | | | | || || ||| | | | | || | | ||| | || ||| | || ||||| || ||||| |||||||||| | | || | || || ||||||||||||||||||| ||| | ||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||
gtatgtatctagcttattcctta-gcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaattt--gtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatag----atagaaatattgaatcttata-----tgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
||| || |||| | || || || |||| | | || || || || || | | ||| | || || | ||| | ||| | || | ||| || | ||| | || ||| | |||||||| || ||||| |||||||||| | ||| ||| || ||||||||||||||||||| ||| | ||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||
gtatgtatctggcttattccttaatg-attggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgt--gtatcatatgagggcgcatgatgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaaagtaaacaattctgctttctactgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
||||||| || || | || || | || | | || || || | | | || | | || | ||| || || ||| | | |||| || | ||||| || |||||||| |||||||| |||| || ||||| || |||||||||||||| |||||||||||||| ||| ||||||| || ||
-------------------------------------------------------------------------tctatcattggta---gaacaagaactcaaaactattg---ctgtatatttttatgtttgga------ttttgtccttttttatttatgttctcatgtg----gaaattaa--tgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
|| || | || | | |||| || | || | || | ||| | | || | || || | || | || ||||||| ||| | |||||| || ||||| || |||||||| || ||||| |||| |||||||| ||||||||||||||||| |||||||| ||||| ||| ||||||| || ||
---------------------------------------------------------------------------gtggatggattatggattggaacttc--aaacttctgcttat-actctttgtt--ttgattatatccattgtatgttctcatgtaaaagattatatgttttgt-----------agGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
|| ||| |||| || | | ||||| | | | |||| | | || | ||| || || ||| | | |||| || ||||||| || |||||||| |||||||| |||| || ||||| || |||||||||||||| |||||||||||||| ||| ||||||| || ||
--------------------------------------------------------------------------------ctctatcttgggtagaact---ggaactcaaaactattgctgtatatt--ttatgtttgtattttgtccctttttatttatgttctcatgtg----gaaattaa--tgtagGATCCATTCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctat-----agGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
|| | | || | | || | | ||| |||| || ||||| || || | | | || | | || | | | ||| ||| |||| | || ||||| |||||||| ||||||||||| |||| ||||| ||||| || ||||||||||| || |||||||| || | || || | || ||
-------------------------------------------------------------------------------------------ataatgcatttgttctttctgct--tggcactatgctactaataaaaa-atc--atggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatctta-tatgatttatgattcacctata-gGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
|| || | | || | | || | | ||| | || | ||| | | ||| | |||| | | || | |||| | | | ||||| | ||||| |||||||| ||||||||||| |||| ||||| || ||||| ||||||||||| || ||||||||||| ||||||| || |
--------------------------------------------------------------------------------------ttcctataatgcat-tgttctttctgctta--gcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatctta-tatgatttatgattcacctata-gGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
| || | | || | | || | | ||| | || | ||| | | ||| | |||| | | || | |||| | | | ||||| | ||||| |||||||| || |||||||| |||| ||||| || ||||| |||||| |||| || ||||||||||| | || || || ||
---------------------------------------------------------------------------------------tcctataatgcat-tgttctttctgctta--gcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
| | | | | || | | |||| || | || | || | ||| || | | ||| || | || ||| |||||| ||| | |||||| || ||||| || |||||||| || ||||| |||| || ||||| ||||||||||||||||| ||||| || ||||| ||| ||||||| || ||
-----------------------------------------------------------------------------tgaaagagaatggattggaacttc--aaacttctgcttat-actctttgttgtgattatatccattgtatgttctcatgtacaaaattatatatgttttgt-----------agGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttat---atgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
| | | || | | || ||| | ||| | | | | | | ||| ||| | ||| || | ||||| || | | ||||| | || ||||| || ||| |||| || ||||| |||| || || || || ||||||||||| || |||||||| ||||||||||| |||||||| ||
-------------------------------------------------------------------------------------------atggtttactagagatactgactccctgctttttga---taaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
| | || | | || ||| | || | | || | | | |||| ||| ||| | || ||| | | || ||| |||| | || ||||| |||||||||||||||||||| |||| ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||| || ||
---------------------------------------------------------------------------------ttgactgatagcatcaatt-tgagaattgtgattagaaaatttcattatggttggtggtatttaat-------gttatctggtatttaatggt--gttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATAMapped 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|87009749|gb|CI310852.1|CI310852EST: GGTTTATGAATTCATGCCTCGTGCAAGTTTAGATCACCATCTATTCAGAA GGTCTCTTCCTCTCCCTTGGTCCATCAGAATGA
genomic: GGTTTATGAATTCATGCCTCGTGGAAGTTTAGATAACCATCTATTCAGAAgtacgtgtct ... tcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGA
EST:
gi|113930919|gb|DQ884020.1|DQ884020EST: AATTCATGCCTCGTGGAAGTTTAGATAACCATCTGTTCAGAA GGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAG
genomic: AATTCATGCCTCGTGGAAGTTTAGATAACCATCTATTCAGAAgtacgtgtct ... tcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
71 (upstream exon),
62 (downstream exon)
Score:
22AATTTGGTGAGGCTGATTGGATATTGTGTTGAAGATGACCAAAGATTGCTGGTTTATGAATTCATGCCTCGTGGAAGTTTAGATAACCATCTATTCAGAAgtacgtgtct ... tcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
ttcacct CT-rich tract
ttaaatagatagaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC