Sequence
atgc intronic sequence ATGC exonic sequencegtacaatgaagagccatataatatactcagtccatactgaaaattgttgttgttcaccttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g42490.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G123140_T02 (Zea mays), 3'ss of exon 8
-------gtacaatgaagagccatataatatactcagtccatactgaaaattgttgttgttc-----accttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
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gtactacctatatttacgatttcaaacatgcatcgcatcgttttggttctttgtttctgttgcaacaagCTTGAGATTAGTAGTG-TCTTCATGGATGTTTTAA-TTTTGCAGCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT
upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 9
gtacaatgaagagccatataatatactcagtccata----ctgaaaatt--gttgttgttcaccttataattcgttgtggtc-------------------atgtttgttaatttgccttttg-cagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
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--gtagtgcaaacccatgtatcagatccaatctgcaatcatttataattcaattaatactcaactattaatccattgcattttttaacggttaactgatgaatatctatttttttattttttggcagATGGATACTCTTTCAAACGGGAACTCATTGAATGAAGTGGCTCATATTGCAAATGGCTCACATCCAGGAAACTGCATTTCTCTTCTTCGCATAAAT
upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 9
gtacaatgaagagccat-ataat---atactcagtccatactgaaaattgttgttgttcaccttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
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--gtagtgcaaaccctttacaattcaatattcaactcttaatcc--attgc-attttttaacggttaactgatgaatatccactttcttttttcttttttgtcagATGGATGCTCTTTCCAATGGGAACTCATTGAATGAAGTGGCTCATATTGCAAATGGCTCACATCCAGGAAACTGCATTTCTCTTCTTCGCATAAAT
upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G46880.1 (Arabidopsis thaliana), 3'ss of exon 8
gtacaatgaagagccatataatatactcagtccatactgaaaattgttgttgttcaccttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
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--------------------------gtaaacaaaaactagagtcttctctctgttcttgatg--ccaaaaccctaagatttttcgattttttccctgcagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCGCAAATGGTTCACATCCTGGAAATTGCATCTCTCTTCTTCGAATCAAT
upper sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv02s0012g02030.t01 (Vitis vinifera), 3'ss of exon 9
gtacaatgaagagccatataatatactcagtccatactgaaaattgttgttgttcaccttataattcgttgt---ggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
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---------------gtttgattcagaca-taattctttcaaatcttcaagacacatcctaaaacccatactcaagactaaaaatgataacttgtattttgcagCTTGATGTTCTTTCCAATGGGAATTCCTTACATGAAGTGGCACACATTGCCAATGGCTCTCATCCAGGAAACTGCATTTCTCTTCTTCGCATCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgttcaccttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
tgttaat putative branch site (score: 3)
tttgcctttt CT-rich tract
atgtttgttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatgaagagccatataatatactcagtccatactgaaaattgttgttgttcaccttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA