Sequence
atgc intronic sequence ATGC exonic sequencegtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g50040.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
-----------------------gtacgtattctcgtcctataacttggcgttaagaatgtac--tactggtgaagcagcat---tgtgatttgtga-gtaacctgctgtggccgcgtg-tagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
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gtacgtgcaccgacccagtccgactaataaatcactctctatag-ttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaag--cagcattgtgatttgtgagtaacctgctgtg-gccgcgtgt--agGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
||| || |||| || || | | | | |||||| | || | || | || ||||| |||| | | || | | | |||||||||||| |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| || |||||||| | ||||||| |
gtaagt-ttcttgttctgtta--------tgaaaatgtag-attgatagagaatatgatgatgattaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgag--taacctgctgtggccgcgtgt-agGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
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gtaagtttttctgt--------tttgttctgaaagggtaata--ggtagagaaa-atgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
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gtaagtctactctactaaca--tacatttcaaacttctccttcttctaat----ctctaacttttccgacgatatttcaaaaatctc----agGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------gtacgtattctcgt-cctata-acttggcgtt---aagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
| | |||| || ||| || |||| | | | || || ||| |||| | | | ||| | || || | ||| |||| || |||| ||||||||||||||||| || |||||||| ||||||||| | || ||||| |||| | | || |||| ||||| | | || |
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacga---tggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtattctcgt-cctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
||| | | || | || |||| ||||| | || ||| | | || | | | | | |||| || ||||| | | || ||||| |||||||| | ||||||||||| ||||| || |||||||||||||||||| |||||| |||||||| | || | || |
----gtaccttagaatcttttgct---cgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttc-gctgctgct-----cagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT
upper sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtattctcgtcctataacttgg-cgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
| | | || ||| |||| ||||| | || ||| | | || | | | | | |||| || ||||| | | || ||||| |||||||| ||||||||||||| ||||| || |||||||||||||||||| |||||| |||||||| | || | || |
-------gtaccatagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcgattttc-gctgctgct-----cagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
gagtaac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgagtaacctgctgtggccgcgtgtagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT