Sequence
atgc intronic sequence ATGC exonic sequence...ttcaacttgttctgactgcaattttgtttgaattaaaggtcacgaaatcagcacattttggtatattcacatacaaatatgttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g41490.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G080176_T01 (Zea mays), 3'ss of exon 16
-ttcaacttgttctgactgcaattttgtttgaattaaaggtcacgaaatcagcacattttggtatattcacatacaaatatg-ttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
| || || | | | | | ||| || | || || || | | || | | |||| | ||| | |||||| |||||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||| || || || |||||||| || |||||||| ||||||||||||||||| || |||
aatgaatctgccatttttactttataatttcaaaatgaagt--agatatttaaatttgttaacacaaaaacattctgataaggttttgtcttccatttgcagGCTAAAGGTTTTGTTGCTAATTCATTCTATACTGGTTTGACTGCTACTGAGTTTTTCTTCCACACAATGGGTGGACGAGAAGGTCTTGTTGACACGGCG
upper sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 14
-------ttcaacttgttctgactgcaattttgtttgaattaaaggtcacgaaatcagcacattttggtatattcacatacaaatatgttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
|| || | | | || ||| | ||| || | || || | || | | |||| ||||| | | | | ||||| ||||| ||||| |||||||| || || | ||| ||| | || || || || ||||||||||| ||||| ||||||||||| |||||||||||||||
gctcagttttaaatatctattgttg-aatactaccctggttat--gtgaaacaactgacagttgtttcttagattgaatactgatatgc----tgtccttgatgcagGCAAAAGGTTTTGTTGCTAATTCCTTTTACAGTGGATTGTCAGCTACTGAGTTTTTCTTCCATACAATGGGAGGGCGAGAAGGGCTTGTTGATACAGCG
upper sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 17
ttcaacttgttctgactgcaattttgtttgaattaaaggtcacgaaatc---agcacattttggtatattcacatacaaatat-gttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
| | || | || | || | ||| || | || || | | | | || | | | | || | | ||||| ||||| ||||| |||||||| ||||| | ||| | |||||||| ||||| ||||| || || |||||||| ||||||||||| ||||||||||||
----aggcttcttgggcatcaccttatgggatcctgattacactaacttctggttactactttgagagctaggaccctgatctcatgtcttcttgccatcgcagGCGAAAGGTTTTGTTGCTAATTCGTTCTACAGTGGTCTTACTGCCACAGAATTTTTCTTTCACACTATGGGTGGACGAGAAGGTCTAGTTGATACAGCG
upper sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv06s0004g03740.t01 (Vitis vinifera), 3'ss of exon 16
ttcaactt-gttctgactgcaattttgtt-tgaattaaaggtcacgaaatcagcacattttggtatattcacatacaaatatgttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
| ||| ||| || | ||| | | || | | | | | || | | | | || || ||||| ||| || | ||||| ||||| ||||| || | ||| ||||||||||| ||||| || || || || ||||| ||||| ||||| || |||||||||||||||||||| |||
cagatctttgttatgtatccaaatgattaatgcactgactgcctattgatagctatgaactttcaaaagcatttaatggaatgtt--gtaatcttaatgcagGCTAAAGGTTTTGTTGCCAGTTCATTCTATACTGGTTTGACAGCTACAGAGTTTTTCTTTCATACAATGGGAGGACGAGAAGGTCTTGTTGATACGGCGMapped 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|33794691|gb|CF323231.1|CF323231EST: TCATAGATCGAACTCTTCCCCACTTTCCTATAAATTCAAAGACTCCTGCA GCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAA
genomic: TCATAGATCGAACTCTTCCCCACTTTCCTATAAATTCAAAGACTCCTGCAgtaagaacat ... ccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAA
EST:
gi|58667561|gb|CK056247.1|CK056247EST: TCATAGATCGAACTCTTCCCCACTTTCCTATAAATTCAAAGACTCCTGCA GCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAA
genomic: TCATAGATCGAACTCTTCCCCACTTTCCTATAAATTCAAAGACTCCTGCAgtaagaacat ... ccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAA
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:
59 (upstream exon),
55 (downstream exon)
Score:
9TGCATGTGTTGGCCAACAATCAGTTGGAGGGCGTCGTGCCCCGAATGGCTTCATAGATCGAACTCTTCCCCACTTTCCTATAAATTCAAAGACTCCTGCAgtaagaacat ... ccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcagcacattttggtatattcacatacaaatatgttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
ttccatttcc CT-rich tract
aaatatgttttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaacttgttctgactgcaattttgtttgaattaaaggtcacgaaatcagcacattttggtatattcacatacaaatatgttttgtattccatttccagGCCAAAGGCTTTGTCGCTAATTCTTTCTATACTGGCTTGACTGCCACCGAATTCTTCTTCCATACGATGGGTGGGCGAGAAGGTCTTGTTGATACAGCG
- - - ttgttct
- - - - - - -gactgca
- - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - cacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - gcacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg