Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacattttaccactgatcttcttatgattgtaacatcaatatgaatcctactattaacttgtcttatatttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g22470.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g22470.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv10s0092g00570.t01 (Vitis vinifera), 3'ss of exon 19
-----gtaagaacattt----taccactgatcttcttatgattgtaaca-----tcaatatgaatc-ctactattaacttgtcttat----atttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
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gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
upper sequence: LOC_Os04g22470.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv10s0092g00710.t01 (Vitis vinifera), 3'ss of exon 22
----------gtaagaacattttaccactgatcttcttatgattgtaacat----caatatgaat--cctactattaacttgtcttatatt---tttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
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atttctttgaatttttaggccttattgttgaatttgtacctataataacatatcttaatctaattgacctccactaagcgaattttatgtaaaattccagTGGCTATCTGGCACCAGAGTATGCAATGCGCGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGTGTAGTGGCTCTAGAGATCCTCAGCGGGAGA
upper sequence: LOC_Os04g22470.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv10s0092g00470.t01 (Vitis vinifera), 3'ss of exon 21
-------gtaagaacat--tttaccactgatcttcttatg----attgtaacatcaatatgaatc--ctactattaacttgtcttat----atttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
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ttttagatttggaatatgccttcttatttaaattcataggcctcattacaagccttcattgaattaacctcaactaagctattttgatgcaatcttgaagTGGATACCTAGCACCAGAGTATGCAATGCGAGGGCATCTGACAGAAAAAGCTGATGTCTTTGGATTCGGTGTTGTTGCTCTAGAGATCCTCAGTGGGAGG
upper sequence: LOC_Os04g22470.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
----------gtaagaacattttaccactgatcttct---tatgattgtaa-----catcaatatgaatcctactattaacttgtcttatat---ttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
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aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccacta--agccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgattgtaacatcaatatgaatcctactattaacttgtcttatatttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
tattaac putative branch site (score: 1)
tattttt putative PPT
tactattaacttgtct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacattttaccactgatcttcttatgattgtaacatcaatatgaatcctactattaacttgtcttatatttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA