Sequence
atgc intronic sequence ATGC exonic sequence...cttaaatgcttttgtgaatccgtcataaggcaattcatcaaaagcatttatattctgtagtttgctccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g47380.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
----cttaaatgcttttgtgaatccgtcataaggcaattcatcaaaagcatttatattctgtagtttgctccctccggtttaatcaaccttggtgtccata-cagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
| || || |||| | | | | ||| | | || || | | | |||||| || || |||| || | | || ||||||| |||||||| ||||| |||||||| || |||||||||||||| || || ||
gtttcgtagatatcaaggtga-tgcataaaaagtaaggcc--taattatgcccttagttttctggttgctctttctagt--aatccactggtatatgtttaatagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
upper sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA14G39890.1 (Glycine max), 3'ss of exon 13
cttaaatgcttttgtgaatccgtcataaggcaattcat-caaaagcatttatattctgtagtttgc-----tccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
|||| | | | | | |||| || | | ||| || | || | ||||| | || | | |||| | | || ||||||||||||| ||||| ||||| ||||| || || |||||||||||||| || || ||
----aatgttataatagacggtccttaagtcattatgtacaacgaaatctgtaattactagttagtggaagtctgaaagatctaat--atgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG
upper sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------cttaaatgcttttgtgaatccgtcataaggcaa----ttcatcaaaagcatttatattctgtagtttgctccctccggt------------ttaat-------caaccttggtgtcca---tacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
| | | ||| | | | | ||||| || | | | ||| | || | ||| || | | | ||| | || || | | || | |||||||| ||||| || ||||| ||||| ||||| |||||||||||||| || || ||
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG
upper sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ27746 (Selaginella moellendorffii), 3'ss of exon 13
cttaaatgcttttgtgaatccgtcataaggcaattcatcaaaagcatttatattctgtagtttgctccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
| | || | ||| | | | ||||| | | || | | | ||||||| |||||| | ||||||||||| ||||||||||| ||||| || | || |
-----------------------------------------------gtgcagactcaaagttggttctttgcgtttact--atctcagctttc---tagGCTGGAACATACGTTAAGGAGTTTGTTCACGGAGATCTAGGACGAACGTATCCGAA
upper sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ37198 (Selaginella moellendorffii), 3'ss of exon 9
cttaaatgcttttgtgaatccgtcataaggcaattcatcaaaagcatttatattctgtagtttgctccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
| | | | | || ||||| | ||| | | | | || ||||||| |||||| | ||||||||||| ||||||||||| ||||| || | || |
---------------------------------------gtgcagactcaaagttggttctttgcgtttacaacgctaactatctcagctttc----tagGCTGGAACATACGTTAAGGAGTTTGTTCACGGAGATCTAGGACGAACGTATCCGAAMapped 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|25806086|gb|CA762047.1|CA762047EST: AAAAAATTTCTGGCGGGTCAAACTATTACCTGTTGCATCTATGCACTCAA GCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACAC
genomic: CAAAAATTTCTGGCGGGTCAAACTATTACCTGTTGCATCTATGCACTCAAgtaagcattg ... gtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACAC
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:
40 (upstream exon),
74 (downstream exon)
Score:
3GATGGAGATTGCAAAAATTTCTGGCGGGTCAAACTATTACCTGTTGCATCTATGCACTCAAgtaagcattg ... gtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatattctgtagtttgctccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
gtttaat putative branch site (score: 3)
tttaatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttaaatgcttttgtgaatccgtcataaggcaattcatcaaaagcatttatattctgtagtttgctccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - aatgctt
- - - - - - - tgaatcc
- - - - - - - - - - - - - - - - - -catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaac