Sequence
atgc intronic sequence ATGC exonic sequencegtatcttgaagtttcagtcaaaccataacattgcgtactctatttatctatggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39380.3 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G074572_T01 (Zea mays), 3'ss of exon 15
gtatcttgaagtttcagtcaaaccataacattgc-gtactctatttatctatggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
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-------------------gtattgtgaaatttcagtttactatttgtctgttccttccataccctccc-tgt----atttttcctaagtttccttttgcagCTTTGATTGAGTCTGACGCAGAAGGCATCGGGGGAAGTGGCTTTGTTGAATGCATCAGAGAGCATATTCATTCG
upper sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G04510.1 (Glycine max), 3'ss of exon 15
-------------------------gtatcttgaagtttcagtcaaaccataacattgcgtactct----atttatctatggctgccataccttcc--catgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
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gtattatgttatgtcacatctcaattcttgctaatacttgtgtggagaaaacattttgtttgttgccagaaattattctgtattgcaagtctggagagcttgtcaaaaagtga-ttgaggttggttttgcagCTTTGATTGAATCTGATGCAGAGGGGATTGGCGGTAGTGGATTTGTTGAATGTATAAGAGAGCATATACATTCG
upper sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 15
--gtatcttgaagtttcagtcaaaccataacattgcgtactctatttatcta-tggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
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gtatgtatctaaggtccaaaatctatttaatgaaaattaatctgcttgaatggtggtttttggagtcttgcaaatgaataagtattttctattg-tttttgcagCTTTGATTGAGTCTGATGCGGAAGGAATTGGCGGTAGTGGATTTGTTGAGTGTATAAGGGAGCACATACATTCA
upper sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ09845 (Selaginella moellendorffii), 3'ss of exon 15
gtatcttgaagtttcagtcaaaccataacattgcgtactctatttatctatggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
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----------------------------------------------------gtaagatctcgttctcattacgtagtgctcctaagctttttttctgcagCTTTGATTGAGTCCGATGCGGAAGGTATTGGTGGAAGTGGATTTGTTGAGTGTGTCAGGGAGCATATTCACTCG
upper sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ15218 (Selaginella moellendorffii), 3'ss of exon 15
gtatcttgaagtttcagtcaaaccataacattgcgtactctatttatctatggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
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----------------------------------------------------gtaagatctctttctcattacgtagtgctcctaagctttttttctgcagCTTTGATTGAGTCCGATGCGGAAGGTATTGGTGGAAGTGGATTTGTTGAGTGTGTCAGGGAGCATATTCACTCGMapped 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|58605330|gb|CK033363.1|CK033363EST: TGGAGCAACTGAGGATCCCCTTTCATCATTTGAATATGGCACCATTCTTG CTTTGATTGAGTCTGACGC
genomic: TGGAGCAACTGAGGATCCCCTTTCATCATTTGAATATGGCACCATTCTTGgtatcttgaa ... ctctttgcagCTTTGATTGAGTCTGACGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
acataac putative branch site (score: 3)
cttttatttctctttg CT-rich tract
aacataacttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttgaagtttcagtcaaaccataacattgcgtactctatttatctatggctgccataccttcccatgtcccaacataacttttatttctctttgcagCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA