Sequence
atgc intronic sequence ATGC exonic sequencegtttctatctcctgtcatccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g37740.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 9
gtttctatctcctgtca--tccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
|||| |||| || ||| | | | | || | | | ||| |||| || |||||| | || | || ||||||||||||| ||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||
gtttgcatctgctatcaaatgccatgaaaccactggtgatactttgtagactaatgtttttctt----tcccttttgatccaagATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
gtttctatctcctgtca-----tccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
|||| |||| || ||| | | | || | | | ||| | |||| ||| || || | ||| | || ||||||||||||| ||||| ||||| || |||||||||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||||||||
gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtaggctgaat-gttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
------------------------------gtttctatctcctgtcatcc-attagagacagtaa--tttaggtctgtggactgatccatttcttgtttttttttcttat-------tatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
||| | | | || | || ||| || || | ||||| ||| || || | | |||| |||| ||||| | ||||| ||||| || ||||||||||| |||||||||||||||||||| |||||| || || |||||||| |||||||| ||||||||||||
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 9
--------------------gtttctatctcctgtcatccattagaga-cagtaatttag-gtctgtggactgatccattt---cttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG-
| | | | | | | | | || | | | || | |||||| | || | | || || | | ||||||| ||||| ||||| || ||||||||||| | ||||||||||||||| || | ||||| || || |||||||||||||| || |||||||| |||
taaagttaattgtgttctttatccttgtgttttataagcttcttgaaagttgcatcctattggttgtggattatagaatctgagtgtaattattatgtgcactatagaTCTTGGGAACACCGACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAGG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
-------------------------------------gtttctatctcctgtcatccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttatt---atagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
|||| | | |||| | || | | | || |||||| | | | || | | ||| || || | |||||||||||| ||||| || ||||||||||| |||||||||||||||||||| |||||| || || |||||||| |||||||| ||||||||||||
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaa-gttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
--------------gtttctatctcctgtcatccattagagac--agtaatttaggtctgtggact--gatccatt---tcttgtttt--tttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
||| | | ||| | || || | | || |||| | | | |||| ||| | | || | | ||||||| ||||| |||||||| ||||||||||| | ||||||||||||||| || | ||||| || || |||||||||||||| || |||||||| |||
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 9
----------gtttctatctcctgtcatccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
| | | |||| || || | | | | | || || | | | ||||| | || | | |||||| |||||||||| || ||||||||||| | ||||||||||||||| || ||| ||||| || || || || |||||||| ||||||||||||
gtttgctatcaagtggcttttctgttattcactttcttttcttaatattataggtcagctaagcaggatgttgttgcatgttat-gtcttagATTCTGGGTACACCCACCAGAGAAGAAATTAAGTGCATGAATCCAAATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtttctatctcctgtcatccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
|| || | | | || | || ||| || | | || || | || ||| | || | || ||||| || ||| | || ||||||| ||||||||||||||||| | || || || ||||||||||| ||||| ||||| |||||||||
gtacgcatgcattcttgctcttttttttctgtttttt----ttgcgagtcgctcttgctcaagacttgcttt-----tgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG
upper sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtttctatctcctgtcatccattagaga-cagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
||| |||| | | | ||| | || | | || || | || ||| | || | || ||||| || ||| | || ||||||| ||||||||||||||||| | || || || ||||||||||| ||||| ||||| |||||||||
----------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgcttt-----tgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGMapped 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|88580059|gb|CI692059.1|CI692059EST: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAG ATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
genomic: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAGgtttctatct ... cttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
EST:
gi|88361945|gb|CI682122.1|CI682122EST: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAG ATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
genomic: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAGgtttctatct ... cttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
EST:
gi|426398|gb|D22261.1|D22261EST: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAG ATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
genomic: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAGgtttctatct ... cttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
EST:
gi|58679635|gb|CK068322.1|CK068322EST: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAG ATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
genomic: CTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAGgtttctatct ... cttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTAT
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),
60 (downstream exon)
Score:
43CCTCTGTTCCCTGGAGAAAGTGGTGTTGATCAACTGGTGGAAATAATAAAGgtttctatct ... cttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
gactgat putative branch site (score: 43)
tccatttcttgttttt CT-rich tract
atttcttgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctatctcctgtcatccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA