Sequence
atgc intronic sequence ATGC exonic sequence...acatactttgtgtgacttgctatcctaattgagttttgtctgtggcttctgtacttgaactaactatacctgtaatattctttgtgtttgcaatttgcagGGTTTCAGAAAGATTGATCCTGACAGATGGGAATTCGCGAATGATGGTTTCCTGAGAGGCCAGAGGCATCTTCTAAAGATGATTAAGAGGAGGAGACCAT
Basic information
| species | Oryza sativa |
| transcript | LOC_Os03g06630.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g06630.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165972_T02 (Zea mays), 3'ss of exon 1
acatactttgtgtgacttgctatcctaattgagttttgtctgtggcttctgtacttg-aactaactatac-ctgta-atattctttgtgtttgcaatttgcagGGTTTCAGAAAGATTGATCCTGACAGATGGGAATTCGCGAATGATGGTTTCCTGAGAGGCCAGAGGCATCTTCTAAAGATGATTAAGAGGAGGAGACCAT
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attggctcagcgtcggcatttgtcgattcttagtgtg--tgatggcttctggaaatgcagcttactgaacgctgcgcgtgttcatcgc-tttgcgacgtgcagGGCTTCAGAAAGATCGACCCGGACAGCTGGGAGTTCGCGAACGAAGGATTCCTGAGGGGCCAGAGGCATCTTCTCCGGCTGATCAAGCGTCGAAGGCCGG
upper sequence: LOC_Os03g06630.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165972_T03 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------acatactttgtg---tgacttgctatc----ctaattgagtttt-gtctgtg---gcttctgtacttg-aactaactatac-ctgta-atattctttgtgtttgcaatttgcagGGTTTCAGAAAGATTGATCCTGACAGATGGGAATTCGCGAATGATGGTTTCCTGAGAGGCCAGAGGCATCTTCTAAAGATGATTAAGAGGAGGAGACCAT
| | |||| || || || | | || | || || |||| ||||||| | || | || ||| || ||| | ||| | | ||||| | ||||||| ||||||||||| || || ||||| ||||| |||||||| || || |||||||| ||||||||||||||||| | |||| ||| | | || ||
gtataccactgcccgtgcctgtaaattcggtcgcaaaacttatgtgaaacctaaagttttacataaatttgccatcttgtcttgttaattggctcagcgtcggcatttgtcgattcttagtgtgtgatggcttctggaaatgcagcttactgaacgctgcgcgtgttcatcgc-tttgcgacgtgcagGGCTTCAGAAAGATCGACCCGGACAGCTGGGAGTTCGCGAACGAAGGATTCCTGAGGGGCCAGAGGCATCTTCTCCGGCTGATCAAGCGTCGAAGGCCGG
upper sequence: LOC_Os03g06630.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0179g00150.t01 (Vitis vinifera), 3'ss of exon 1
acatactttgtgtgacttgctatcctaattgagttttgtctgtggcttctgtacttgaactaactatacct-gtaatattctttgtgtttgcaatttgcagGGTTTCAGAAAGATTGATCCTGACAGATGGGAATTCGCGAATGATGGTTTCCTGAGAGGCCAGAGGCATCTTCTAAAGATGATTAAGAGGAGGAGACCAT
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tgctaaatcaagtg-cctgaaatcctttgatgggtcgatgtgaagtatctatccactggttcttgaaatttcatcctaaatatggaatttgatctctacagGGTTTTAGAAAGATTGATCCGGACAGATGGGAGTTTGCAAATGAAGGATTCATCAGGGGTCAAAGACATCTCCTTAAGAACATCAGGAGAAGAAAGACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctgtacttgaactaactatacctgtaatattctttgtgtttgcaatttgcagGGTTTCAGAAAGATTGATCCTGACAGATGGGAATTCGCGAATGATGGTTTCCTGAGAGGCCAGAGGCATCTTCTAAAGATGATTAAGAGGAGGAGACCAT
aactaac putative branch site (score: 1)
taatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatactttgtgtgacttgctatcctaattgagttttgtctgtggcttctgtacttgaactaactatacctgtaatattctttgtgtttgcaatttgcagGGTTTCAGAAAGATTGATCCTGACAGATGGGAATTCGCGAATGATGGTTTCCTGAGAGGCCAGAGGCATCTTCTAAAGATGATTAAGAGGAGGAGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - gcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg
