Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacaaatcaacatttgtcttcatacaactataacttctaaatgaatgctacttttaactcgtttgatctttgtgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g17050.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g17050.1 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv10s0092g00710.t01 (Vitis vinifera), 3'ss of exon 22
-------------gtaagaacaaatcaac--atttgtcttcatacaactataactt---ctaaatgaatgctacttttaactcgtttgatctttg--tgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG---------------------------
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atttctttgaatttttaggccttattgttgaatttgtacctataataacatatcttaatctaattgacctccact--aagcgaattttatgtaaaattccagTGGCTATCTGGCACCAGAGTATGCAATGCGCGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGTGTAGTGGCTCTAGAGATCCTCAGCGGGAGA
upper sequence: LOC_Os05g17050.1 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv10s0092g00470.t01 (Vitis vinifera), 3'ss of exon 21
-------gtaagaacaaatcaac--atttgtcttcataca----actataacttctaaatgaatgctactt---ttaactcgtttgatct--ttgtgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG---------------------------
| ||| | | | |||| |||||| | || || | | ||||| || | | || |||||| | |||||||| || ||||| || |||||||||||| |||| | | |||||||||| |||||||| |||| ||| || ||
ttttagatttggaatatgccttcttatttaaattcataggcctcattacaagccttcattgaattaacctcaactaagctattttgatgcaatcttgaagTGGATACCTAGCACCAGAGTATGCAATGCGAGGGCATCTGACAGAAAAAGCTGATGTCTTTGGATTCGGTGTTGTTGCTCTAGAGATCCTCAGTGGGAGG
upper sequence: LOC_Os05g17050.1 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
---------------------gtaagaacaaatcaacatttgtcttcatacaactataacttctaaatgaatgctacttttaactcgtttgatctttgtgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG---------------------------
|| ||| | | | | | | | || | || || | ||| | | | | | ||| ||||| ||||| || || |||||||||||| | || | | ||||||| |||||||||||||||| |||||| ||
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttcc---agTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaactataacttctaaatgaatgctacttttaactcgtttgatctttgtgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG
tctttgt CT-rich tract
tataacttctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacaaatcaacatttgtcttcatacaactataacttctaaatgaatgctacttttaactcgtttgatctttgtgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG