Sequence
atgc intronic sequence ATGC exonic sequencegtacgaacaagcccatgattggttagcttttcttatattctgaatttatgatccagtaacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g34750.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G071304_T01 (Zea mays), 3'ss of exon 5
gtacgaacaagcccatgattggttagcttttcttatat-----tctgaatttatg---atccag--taacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
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gtatcatcaatcctcacggcgtttagctcttctagtataatacttttgacccatgctcatctaagtcaacacttcataattttgaatttagATACATTGCATGGAGGATGGTTCAGTAGAGATTTATAGTCGCAATGCTGAAAGAAACACCGGAAAGTATCCAGATGTTGTTGATGCAGTTTCTAG
upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G08600.1 (Glycine max), 3'ss of exon 5
gtacgaacaagcccatgattggttagcttttcttatattctgaatttatgatc--cagtaacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
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----gtgatactacatggtcaaattttccatcagaaacatgatacttattatgtgcaataacattagctgtattgaaac--agATACATTACCTGGAGAATGGATCAGTTGAGATTTACAGTAGAAATGCAGAACGGAATACTGGGAAGTTTCCTGATGTTGTTGCCGCTGTTTCAAG
upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G19880.1 (Glycine max), 3'ss of exon 5
----------------------gtacgaacaagcccatgattggttagcttttcttatattctgaatttatgatccagtaacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
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tatagttccggtcctcttctcttcatggtcaaattttccatcaga-aacatggccctcatgatacttattatgtgcaataacattagctgtattgagac--agATACATTACCTGGAGAATGGCTCAGTTGAGATTTACAGTAGACATGCAGAACGGAATACTGGGAAGTTTCCTGATGTTGTTGCTGCTGTTTCAAG
upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0061g00690.t01 (Vitis vinifera), 3'ss of exon 5
------gtacgaaca-agcccatgattggttagcttttcttatattctgaatttatgatcca-gtaacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
|||| | | | ||| || ||| ||||| | | | | |||| |||| | | | || | | | ||||||| | | ||| ||||| ||||| ||||| |||||||| ||||| || | || ||||| ||||||||||||||||||| ||| ||||| ||
gtaatagtacctagataaaccacttctgtttactgtttctccttgtgt---tatatgttccatgctatgact-atgttcatccaagcagATACACTACAAGGAGGATGGGTCAGTTGAGATATATAGTCGCAATGCCGAACGAAATACTGGAAAGTATCCTGATGTTGTTGTTGCAGTTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttcttatattctgaatttatgatccagtaacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
ttatattctgaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgaacaagcccatgattggttagcttttcttatattctgaatttatgatccagtaacacttgatactttggaatgaagATACATTGCCTGGAAGATGGATCAGTAGAGATCTATAGTCGTAATGCTGAGAGGAACACTGGGAAGTATCCTGATGTTGTTGATGCGGTTTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA