Sequence
atgc intronic sequence ATGC exonic sequencegtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g53195.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G000052_T01 (Zea mays), 3'ss of exon 3
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcc--cttgaagtgcat-ttcaaatgttgtgaa---attcttccccactggttattctaatgtggttt----ctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
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gtgattttcggtgttattttttttgtcat-gtttcggtgttggtgtaatgttacaacttacaacctgtatttatttggcgaaaatgagtagaccctttgtgatccttttcaatttgtgtgacacattccagGTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 3
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatccct--tgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
||| | | || || | | | || || | | | |||| || | | || | | ||| | | | | | |||| ||| ||| || |||||| ||||||| ||||||||||| || || ||||| ||| |||||||||| ||||||||||| ||||| || ||| |||||||||| ||
gtatttttcagtgttacttcttgtcatgtttgtgtgttggtgatgcaatcatatttatttgagaaaaatggaaagatccttttgtgatgcatt-tcggttgctctgatgca------tttcagGTTATTCTTCTGGAATCTCGTGATAGAATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCAGTCGATTTGGGAGCATCTTG
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G45140.1 (Glycine max), 3'ss of exon 2
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaa-gtgcatttcaaatgttgtgaaattcttccccactggttattctaa--tgtggtttctttc--cagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
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------------------------------gtattaaagtttttgttttcccctcttgaacatacatacatacttttgt-acttgttaatttatttatttgcataaattgtacttttatttgtcagGTTATTCTTCTAGAATCACGGGAAAGACCTGGTGGCCGAATTCACACTGATTACTCATTTGGCTTTCCTGTTGACCTTGGTGCATCGTG
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 2
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
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-------------taactttcaag--gattgtggtgttgtgtgctgcttaatt--gtaaacttgaacttacatggcctcaa----ttattaaatggtgcctatgttttaatttttggtcagGTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATG
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G03610.2 (Glycine max), 3'ss of exon 2
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaa---gtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
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-------------------------gtattaaagtttttttgttt---tcccctcttgaacatacatacttttgtacttgttaatttatttatttgtataaattgtacttttatttgt---cagGTTATTCTTCTAGAATCACGAGAAAGACTTGGTGGCCGAATTCACACTGACTACTCATTTGGCTTTCCTGTTGACCTGGGTGCATCGTG
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaat-gtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
| | || |||| ||| || | | | | | | |||||||| | |||| | | | | ||||| | | | | ||| | ||||||||||| |||| || | || || || ||||| ||||||||||||||||||| ||||| ||||||||||| ||||||||||| |
------------gaaacttg-aacctacatgt--tgttcgaagccaattattatgcaattatgcatttccagagttgagggacta------aatggttcctttgtttataatttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactg-gttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
|||| ||| | | ||| || | | | || | || ||| | |||| | ||| | || |||| |||| | | ||||| | | || || || |||||||| || ||||| || |||||||||||||||| ||||| |||||||||||||| || ||||| ||
--------------------------gtttgtgatgtttcatgttttata--caatatatcctgatagctgattttg-atatctctttctcacggtgtggttct----tggtgttt----agGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
|| | || |||| || | | | | || || || | || | ||| | |||| || ||| | | | | | ||| |||||||||| | ||||| ||||| || || ||||| | |||| ||||||||||| ||||| ||||||||||| ||||||||||| ||
----------tagccatagataaat--attgctctgttctgtttgctattttcgtttttgatcagatttctgt-ttgctatattc-------ctaactatacacactttatctttttt-agGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
ttctaat putative branch site (score: 2)
tttctttcc putative PPT
ttattctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA