Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06820.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 4
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttacta-aaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
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-----gtaagattacaattcaatggttgtttccaac--------tatcgatacttgttg-aatcctgatcat-gtggtcatgctatttaccttttggtgcttgtataaattatttgatctcaaaacg-tatgcttgttaagaaactgtgtcattttattattgcagGGATAGAGACCGATATGTCCAAGGAGATTATCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAAAAGGAAATG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 6
gtaaggcatagatctatctacgtattcttttgtaaca-gggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttacta-aaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
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gtaagattacaattca---atg-gttgtttcgaactatggatacttgttga-----atcctgatcatg-------tggttgtgctatttaccttttggtgcttgtataaattatttgatctcaaaacg-tgtgcttgttaagaaactgtgtcgttttattattgcagGGATAGAGACCGATATGTCCAAGGAGATTACCGTTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTTAAGACCTGGGCTGAGAAGGAAATG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 4
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaa-caacttgttctaaaaataacttgcatgtgaac-aaactacattattctcttcttg-cagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
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--------------------------------------------------------------------taaatcctaatgtatttctactactttgactggagaagaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttattgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGATTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCAGAGAAAGAAATG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 4
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaac-aaactacattattctcttcttg-cagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
|| ||| | ||| || | | || || ||| | || |||| | ||| | | | ||||| ||| || || || | | | |||||||||||| ||||||| || ||||| | ||| ||| || |||| ||||||||||||||||| |||||||||| || || |||||||| || ||||||
---------------------------------------------------------------taaattg-taatgtatttctactacattgacta---tagacgaagtttcttgattcaaagttgtttgttttatgaactaaattatatgatcttatcgatatcagGGATAGAGATAGATATGTGCAAGGAGACTTCCGGTTTCGAAATGGATACTGCAAGCATAATCCCAGGAAAATGGTAAAAACATGGGCTGAGAAAGAAATG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G37350.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttc-ttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
|| | | | |||| |||| || | | ||| || | || | | | || | | | | || ||||||| |||| |||||||| || ||||||||||| |||||| |||| ||||| || |||||||| || ||||||||||| ||||||||||| ||| |
------------------------------------------------------------------------------------gtgagctat-tagtattacatgaatagaggttgttaatgattttgttttagtcc-ctatttttataactgtgatgatttcagGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCTCGAAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G24990.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
|| | | ||| || | | ||||| |||| | ||||||| ||| ||| | || || || || | ||| |||||| |||| |||||||| || ||||||||||| |||||| |||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||| |
--------------------------------------------------------------gtaagctatttacatgaataatgt-tgtttatcagttcttctaaaact-cttaacttaatcccagttttca------------actttgatgatttc----agGGATCGAGATCGATATGTACAAGGAGATTACCGTTTTAGATATGGCTACTGTCGTCACAATCCCCGGAAGATGGTGAAGACATGGGCTGAAAAAGAACAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g01390.t01 (Vitis vinifera), 3'ss of exon 4
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatg--gatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgca-tgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
|||| | || ||| ||||| || |||| | |||| | || | | | |||| ||| ||| | ||||| || || | | |||||||||||| || ||||| || ||||| ||||| || |||||||| ||||||||||| |||||| |||||||||| ||||| |||||||| || ||||||
--------------------------------------------------------------atatctcaatgatgctgatattgcaaatgatttcca-tttttccaagagtatgtattct----atagcttataatgtgattcgtct-tgttttctaacaactccagGGATAGAGATCGGTATGTACAAGGAGACTACCGTTTCAGACATGGATACTGCAAGCACAATCCTAGGAAAATGGTAAAGACATGGGCTGAGAAAGAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
aaataac putative branch site (score: 2)
cattattctcttctt putative PPT
ttctaaaaataactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcatagatctatctacgtattcttttgtaacagggtactttttgacagctactgcagatatgttgattatggatatgttctgtgttttctagttttactaaaacaacttgttctaaaaataacttgcatgtgaacaaactacattattctcttcttgcagGGATAGAGACCGATATGTCCATGGAGATTACCGCTTTAGACATGGTTACTGCAAGCATAATCCTCGGAAAATGGTGAAGACCTGGGCTGAAAAGGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA