Sequence
atgc intronic sequence ATGC exonic sequencegtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g39640.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 16
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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----------------------------------------------------------------------------------------tagtgatgtatcacatgtcttctttatgtt--gtaactaaactatta---ttttccttgcaaaactaaatg-atgcatatgctaaatttgttgaa-----ttttctttcagGGACGGTGTTAGTGAAGGTCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGGAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 15
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacc-tagtgttt-ttgttcgctatttgaagtatga--aagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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---------------------------------------------------------------------------------------------------agaatggtggtattcattgctagttacgtatattgtaactaaactattcttttctttgctaatctatgtgtatgttaaatttattga----atttctcttccagGGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 8
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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-------------------------------------------------------------------------------agtataaatttatccagatatgtggggatgtattttgttca--aatcaatatctgctaatttccgaaaca---ttctagtt-tgtgttaacgagaaatttgaac--------------agGGATGGTGTAAGTGAAGGGCAATTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 16
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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-------------------------------------------------------------------------------------------agagatgtgggggaatgtatttc-attca--aatcaatatctcctaatt---ttcaaaacattctagtt-tgttgaaactgtttgtgtttgcgagaaatttgaac-agGGATGGTGTAAGTGAAGGGCAGTTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 17
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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---------------------------------------------------------------------------------------------atgtg-tgtgcttacttaggagcatggctttctgaaacatgctagtt--tgatgaaagagt-tagttaccggtatattaacattg--aatgttgaaatttgaacagGGATGGTGTAAGTGAAGGACAATTTTACCAAGTTTTACTTTATGAGTTAGATGCAATTCGGAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 17
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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-------------------------------------------------------------------------------------------gtgtgtgcttacttcggagcatg-gctttctgaaaaacat-tctagtttgacgaaagagtttgctactggcattt----taacattg--aatgttgaaatttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 16
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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--------------------------------------------------------------------------------------------------------gtaa-gtctctctttgctcatttaagtaaaagaattatatctaaaacccacaattagttctcatggttgttttattcgcgc------------agTGATGGAGTAAGCGAAGGGCAATTCTATCAAGTTTTACTCTATGAGTTGGATGCAATTCGAAAG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 16
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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-----------------gtattcttaattt---gcttattcattacag--gtccagtcctactgttttctttctggt--taggacttagagaaaagaaactgttattgtgctattgattgg-gcatgagagacaagactcaagaat---ggtttctgttttt-tgtcttcca-taatat--------------ttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAGMapped 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|29674861|gb|CB671136.1|CB671136EST: GCAAAAGCCATTGAGAATAATTTTCTACAG GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGA
genomic: GCAAAAGCCATTGAGAATAATTTTCTACAGgtatgctact ... tctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGA
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:
63 (upstream exon),
48 (downstream exon)
Score:
6GGAGCTCTTAATATCCTTCAGGAAGGCCACTGGGCAAAAGCCATTGAGAATAATTTTCTACAGgtatgctact ... tctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
tgctaat putative branch site (score: 6)
tactgcttctcttct putative PPT
ttctatttgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC