Sequence
atgc intronic sequence ATGC exonic sequence...caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g01380.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 4
----------------------caattgaagt---gaaacaagc---aagctcacctgattttttttatta---tttag---gcataatctgtattgcattctgatgagtaa-catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
| ||| | || || || ||||| | | | | | ||| | || | | || |||||||||| || || || | ||| |||| ||||| |||||||||||||||||||| || ||||| ||||| || ||| ||||||| ||||||| ||||||||||||||||||||||| |||||||||||||
gtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 12
-------------caattgaagtga---aacaagcaagctcacctgattttttttattatttaggcataatctgtat---tgcattctgatgagtaa---catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
| |||| | || | | | | || ||| | ||| || || || |||| ||||||||||| ||||| |||| | | |||| ||||||| ||||||||||| ||||||||||| ||||| ||||| || ||| ||||||| ||||||| |||||||||||||||||||||||||||||||||||||
gtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacag-caaaaggcgtatgcttgcattctgattagtaaacgcatccaatcatatgtaatgcagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 25
-------------caattgaagtga---aacaagcaagctcacctgattttttttattatttaggcataatct-gta-ttgcattctgatgagtaa---catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
| |||| | || | | | | || ||| | ||| || | || || | |||||||||||| ||||| |||| | | |||| || |||| ||||||||||| ||||||||||| ||||| ||||| || ||| ||||||| | ||||| |||||||||||||||||||||||||||||||||||||
gtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 4
-------------------------caattgaagtgaaacaagcaagctcacctgattttttttattatt-taggcataatctgtattgcattctgatgagtaacatctat--aattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
| | | ||| || ||| | | | || ||| | | | | | || | | ||||||||||||| || || ||| || | | |||| ||||| ||||||||||||||||||||||| ||||| ||||| || ||| ||||||| ||||||| |||||||||||||| ||||||||||||||| ||||||
gtttggttgaaacccattctattgactgataatatgagactagcga--taagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaa-atccatccattcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 7
-------------caattgaagtga---aacaagcaagctcacctgattttttttattatttaggcataatctgtat---tgcattctgatgagtaa---catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
| |||| | || | | | | || ||| | ||| || || || |||| ||||||||||| ||||| |||| | | |||| ||||||| ||||||||||| ||||||||||| ||||| ||||| || ||| ||||||| ||||||| |||||||||||||||||||||||||||||||||||||
gtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacag-caaaaggcgtatgcttgcattctgattagtaaacacatccaatcatatgtaatgcagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 12
caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtat---tgcattctgatgagtaa---catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
| | | | | || ||| | ||| || || || |||| ||||||||||| ||||| |||| | | |||| ||||||| ||||||||||| |||| |||||| ||||| ||||| || ||| ||||||| ||||||| |||||||||||||||||||||||||||||||||||||
-----gtccccgacaatatgggagtagctaattcaatactatatacag-caaaaggcgtatgcttgcattctgattagtaaacgcatccaatcatatgtaatgcagGGTAAGAAAGAATGTTTTGTTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 26
caattgaagtgaaacaagcaagctcacctgattttttttattatttag---gcata-atctgtattgcattctgatgag-taacatctataattgtgtatt---gcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT-
| ||| | | | | |||| ||||| ||| ||||| | || | | | || ||| || | | | | |||||||||||||||||||||||| || ||||| ||| |||| ||||| |||||||| || || |||||||||| | || ||||||||||| ||| | ||||
---------tcttacagtcccatgtattttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaatatttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 27
-----------------------------------------------------------------------------------------caattgaagtgaaacaagca-agctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatct--ataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
|| | || || | | | | | | ||| || || | | | || |||| | | ||||| || || || ||||||||||||||||| || ||||| || || |||||| | |||||||| | || || | ||||||||||||||||| | ||||||||||| ||| | || |
gtgtttattttcttgtccttttccttaagatatcaaactccagtattcgtaaattagatactaactaggttagaccttttggcatagtgcagtgaccctgcttcacttagaaattattttgctgctttctttcttcacctccagtgctggttcttttcttttaattaacaaagggattatattgatttgcagGGAAAGAAAGAGTGTTTTGCATCATGCCTCTTTGTCTGTTATGATATTATACGGCCAGATGTTGCTCTTGAGCTATCTTGGATGAACAATATGATTGATT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 27
----------caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
||| | || | | | | ||| |||||||| | ||||| ||| | | | | | | | || ||| |||||||||||| ||||||||||| || ||||| ||| |||| ||||| ||||| || || || ||| |||||| || || |||||| |||| ||| | ||||
caatcttttttgtttgtcctcgg--gagtgatagtatttcaatttatttattatatgcatataattgagatttc-------taaattttcttttcatatgcttat-gcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATACGGGCAGACATTGTTCTTGAACTAGCTTGGATGCACAATATGATTGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 26
-----caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
|| | | | | || | || | | | || | | | | ||| | | | ||||| ||| | | | | ||| ||| |||||||||||||||||||||||| || ||||| ||| |||| ||||| |||||||| || || ||||||||||| | || ||||||||||| ||| | ||||
tcttacagtcccatgtagtttaattttcttatttgttaatgtgcatactattgac-taaggtcaaatatattctaatgtttc---tttccacatgtttat-gcagGGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAGTTGGCCTGGATGAACAATATGATTGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 25
caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatctataattgtgtattgc-agGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
|| | | | | || || ||| | || | ||| | | | ||| ||| || | ||| | || | ||| ||||||||||| ||||| ||||| |||||| | |||||||| | || || | ||||||||||||||||| || ||||||||||| ||| | || |
tgcttcacctcacctttgttttctttgtcatgcttctttggtcttaattttaaattttaacaaaggagttatgt-taatattattccctgtatctttccagGAGAAGAAAGAATGTTTTGCATCTTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 27
caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatctataattgtgtatt---gcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
|| ||| | | | || | | |||| | || || || ||| ||| ||| | | | | | | | |||||||||||| ||||||||||| || ||||| ||| |||| ||||| | || || || || ||| |||||| || || |||||| |||| ||| | ||||
---ttcaagctttttagtttgtcctaatggagtgatagtatttcaatttatttatgtgcatataattgagatttctaaattttcttttcatatgcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATCTCATACGGGCAGACATTGTTCTTGAACTAGCTTGGATGCACAATATGATTGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 27
---------caattgaag---tgaaacaagcaagctc-acctgattttttttattatttaggcataatctgtattgcattctgatg-agtaacatctataattg--tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
|| || | | | || || | | | | ||| ||| || | ||| || | | | | |||| | | | | ||| | ||||| || || |||||||||||| | ||||||||| | ||||||||||| ||||| | || || ||||| || ||||| ||||| ||||| ||| ||||||
gtatgatgatggttaaacatttacgagatgctagtgctagccattcagtttggttagttgaaaagaattggtccagacgttgaacgtagtatcccgtgtcttctgctgttatacagGGCAAAAAGGAATGCTTTGCTACATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 27
--------------------caattgaagtgaaacaagcaagctcacctgattttttttattattta-ggcataatctgtattgcatt----ctgatgagtaa-----catct--ataattgtgtattg-----------cagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
||| | |||| || | | |||||| | || || | || | ||| |||| || || |||| | |||| | ||| ||||| || || |||||||||||| | ||||||||| | ||||||||||| ||||| | || |||||||| || ||||| ||||| ||||| ||| | ||||
gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgc-attctgatgagtaacatctataattgtgta---ttgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
|| | ||| | | || ||| || ||| | || || | |||| ||| | | ||| || |||| | |||| |||||||||||||||||||||||||| ||||| |||||| | || || ||||| || ||| | || |||||||||| ||||| ||||| ||||| ||||| ||||
---ttaatgtgggcatggttctaatatctt-tttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTMapped 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|12622957|gb|AU173170.1|AU173170EST: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAG GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGNTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
EST:
gi|29685119|gb|CB681394.1|CB681394EST: CTGGTGACCGCAAGCTGTCAAAAGATTTGCTTGTCTATTTCATTGAACAG GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
EST:
gi|29627717|gb|CB632728.1|CB632728EST: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAG GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
EST:
gi|29664581|gb|CB660856.1|CB660856EST: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAG GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
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:
75 (upstream exon),
70 (downstream exon)
Score:
110GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggcataatctgtattgcattctgatgagtaacatctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
gagtaac putative branch site (score: 110)
taacatctataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgcattctgatgagtaacatctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - aagtgaaa
- - - - - - - - agcaagc
- - - - - - - - - - - - cacctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc