Sequence
atgc intronic sequence ATGC exonic sequence...actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g12550.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G167886_T01 (Zea mays), 3'ss of exon 11
------actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
|| | | || |||| || | | || ||| || | ||| | ||| | | || ||| | | || |||| |||||||||||| ||||||||||||||||||||||||||||| | ||||||| | ||| ||||||||||| ||||||||||||||||||||||| |||||||||
cggctaaccctaatgggccggcagcccaacagtggtg-ccggcctacacacactcacac-acata-gtcta---acaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
|| | | ||||| |||| | ||| ||||| | | | ||| | ||| | | | | | | | | || | || ||||||||||| ||||||||||| ||||| | || ||| | || |||||||| || || || |||||||||||||| ||||| | ||||||||
--------gtaaagccttatgct--------actagtacatccatg--ttcagaacttggagatataacacagaact-tgtttgtgtgggccggtc--agATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11
actgtggggttacgatttatgt-gcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttc----tttattgcacttccat-----agGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
| | | |||||| | | || | | ||| | || || || | | || |||||| || | | || || |||| || |||||||| || ||||| ||||| |||||| | |||||||| || ||||| || ||||| || || ||||||||||| ||| | || ||||
----------tgctacttatgttgtgattataggaataaaactcttggattttttatttatttttttatttctattttatttcaactttcaaaatatttttatcatgcagGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------actgtggggttacgatttatgtgcagt---aatgactaatgacctcat--actttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
|||| | | | ||| | |||| | | | | || | || | | | | | | || | | | || ||||| | |||| |||| || |||| ||||| ||||| ||||| ||||| | || |||||||||||||| |||||||| || || |||||||||| ||||| | ||||||||
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactc----agGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------------------------actgtggggtt--acgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
| || || | | || |||| | | | | || | | | | || || || | | ||| | ||| | ||| || | |||| || ||||||||||| ||||||||||| || || | ||||||||||||||||| || ||||| || || |||||||| ||||| |||||||
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgt-cagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------actgtggggt-tacgatttatgtgcagtaatgactaatgacctcatactttca-----ggatataaggctat------gggctaatacta---tttctttattgcacttccat-agGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
| || || | | || | | ||| | | | | | | | |||| | || || |||| | ||||| | || | ||| || |||| || ||||||||||| ||||||||||| ||||| | || |||||||| |||||||| ||||| || ||||||||||| ||||| |||||||
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
| || || | | | | || | | | |||| | ||| || | || | |||||| | ||||| || | || || ||||| |||| ||||||||||||||||| ||||| || || ||||||||| ||| | ||| ||||
---------------------------------------gtttgcgctctctgttttttggact-----ccattgaaattttccttttg---tttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
upper sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ14567 (Selaginella moellendorffii), 3'ss of exon 11
actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
| || || | | | || | | | |||| | ||| || | || | |||||| | ||||| || | || || ||||| |||| ||||||||||||||||| ||||| || || ||||||||| ||| | ||| ||||
---------------------------------------gtttgcgctctctattttttggact-----ccattgaaattttccttttg---tttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGMapped 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|86482193|gb|CI124826.1|CI124826EST: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAG GTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
genomic: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAGgtagatatga ... acttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
EST:
gi|29627251|gb|CB632262.1|CB632262EST: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAG GTGTACAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
genomic: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAGgtagatatga ... acttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
EST:
gi|66915004|gb|CX101852.1|CX101852EST: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAG GTGTACAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
genomic: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAGgtagatatga ... acttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
EST:
gi|29673906|gb|CB670181.1|CB670181EST: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAG GTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
genomic: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAGgtagatatga ... acttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
EST:
gi|58653118|gb|CK041798.1|CK041798EST: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAG GTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
genomic: GCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAGgtagatatga ... acttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAA
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),
68 (downstream exon)
Score:
5AGAGCACATACTACTGGCATATGGTCGTCGTCATAACTCACTTCTGAGGGGCATTTTCATGGATGGCAAGACCACAATCCCTGTGTACACTGTCTTGGAGgtagatatga ... acttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
ggctaat putative branch site (score: 5)
cacttcc putative PPT
taatactatttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG
- - - - - - - - -tatgtgc