Sequence
atgc intronic sequence ATGC exonic sequencegtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g40080.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G154366_T01 (Zea mays), 3'ss of exon 8
gtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
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----------------------gtgagtactccctagca-gcctaataaagaagggttctttgcttctttgatg-------ttctattga----tggtttctctgtcctttgcagGCCATCAAAGATTTATTTCCACACGACTCAAATCCGTTTTATGCTGGATTTGGAAATAGAGACACAGACGAGCTTAGCTACCTCAAGGTTGGTATTCCTA
upper sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G36130.1 (Glycine max), 3'ss of exon 9
gtcagtactcagcaacacaaagataaatatatgaacatacattga-ataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
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-----------------gttaggttcccac-taaactaaaattgacaaaatttatttttttccactatggtcatattattaaacataagtgg----aattttaatgcttc---cagGACATTAAGGCACTTTTTCCTCCAGATTGGAATCCGTTCTATGCTGGTTTTGGAAATAGGGATACCGATGAAGTCAGTTACCTTAAGGTTGGAATCCCAA
upper sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 14
gtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
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---------------------gttagtttcccgctgctacatattataatgag------catattacagtcataatgttattaaagtcaa--tttgaatt-tttatgtcat-cagGACATCAAGGCACTTTTTCCTTCTGATAGCAGTCCATTCTATGCTGGTTTTGGTAATAGGGATACTGATGAAATCAGCTACCTTAAGGTTGGAATTCCCC
upper sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 13
gtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
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---------------------gttagtttcccgctgctacatattacaat-----gatcat-attacattcataatgttattaaagtcta--tttgaatt-tttatgtcat-cagGACATCAAGGCACTTTTTCCTTCTGATAGCAGTCCATTCTATGCTGGTTTTGGTAATAGGGATACGGATGAAATCAGCTACCTTAAGGTTGGAATTCCCC
upper sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
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---------------------gttagttttatgcgggt-ttttttatgtctgttgaactctcat-gtcctc-tgaacta---cgtttaa---ctcggtttttccaaaatatacagGAGATACGGGGCTTGTTTCCTCCCGAACACAACCCATTCTATGCTGGTTTTGGAAACAGAGACACAGATGAGATAAGCTACCTTAAAGTCGGAATCCCCC
upper sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 10
gtcagtactcagcaacacaaagataaatatatgaa-catacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
| | | || | | ||| ||| || | || | | || | | || | || | || ||| || ||| |||| |||||| ||| |||||||| |||| | ||||||||||||||||| |||||||| | || || |||||| |||| ||||| |||||||| ||||| |
---------gtgtatggtctttgtgcatgcccggatcatttgttggatgagtggaaggttaaggatgaa---aaaaggtagctaataatgc-ttttagttccccaatttt---cagGATATCAAGGCATTATTTCCTTCTGATTGCAATCCATTCTATGCTGGTTTTGGAAACCGGGACACTGATGAGTTTAGCTACCTTAAGGTTGGAATTCCAAMapped 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|29667119|gb|CB663394.1|CB663394EST: GAGAAGTTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGG GCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTT
genomic: GAGAAGTTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGGgtcagtactc ... tttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTT
EST:
gi|86900533|gb|CI298368.1|CI298368EST: TTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGG GCTATCAAAGCACTATTTCCTC
genomic: TTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGGgtcagtactc ... tttcacacagGCTATCAAAGCACTATTTCCTC
EST:
gi|58689879|gb|CK078566.1|CK078566EST: TTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGG GCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTT
genomic: TTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGGgtcagtactc ... tttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTT
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:
44 (upstream exon),
68 (downstream exon)
Score:
20TTATCAGACGAGCTCCTCACGAATTCAAGATCTCATGCCTAGGGgtcagtactc ... tttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
tcttgat putative branch site (score: 20)
cctgtttc putative PPT
atgaaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtactcagcaacacaaagataaatatatgaacatacattgaataattgcttgctcttcattgcgctcatgaaataattcgtaccaagtcttgattcacctgtttcacacagGCTATCAAAGCACTATTTCCTCCTGACTCAAATCCATTCTATGCTGGATTTGGAAATAGAGATACAGATGAGCTTAGTTACCTCAAGGTTGGGATTCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT