Sequence
atgc intronic sequence ATGC exonic sequence...gaagcgattaattcgtatcgagagttgataattgatcagattgctaatcaactagtagcagcaatgatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g21300.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g21300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G32350.1 (Arabidopsis thaliana), 3'ss of exon 1
gaagcgattaattcgtatcgagagttgataattgatcagattgctaatcaactagtagcagcaatgatgaatgaattctgat-ggtcaatttggttgtc------agAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
||||| || | || | | | | ||| | | | | || || || || | || | |||||| || | |||||| | || ||||| |||||| |||| ||||||||||| ||||||||||| ||||| | || | | |||| || || || ||| ||||||
-------gtaatttaatcagaaattttaaatcttcttcatttgttcttttatttttaaca-tgattttgttttttcaaaaattgaataatttgatttttgagtatagAGGAAGCACATGTGCCATGCGATGTTGCTAGAGACGGTGGCTGCGGTGCCGGGAATGGTCGGGGGGATGCTTTTGCACTTGAAATCTCTCCGGAGGTTCG
upper sequence: LOC_Os02g21300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------------------------------------------------------gaagcgattaattcgtatcgagag-ttgataattgatcagattgctaatcaactagtagcagcaatgatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
||| || | | || ||| || | | | || | | ||| | || || | || | | | ||| ||| | | ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||||| | || | ||||||| || ||||| || |||||||
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagtttttagtttgctagtcttataaacttggactgattttatttttg-cagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
upper sequence: LOC_Os02g21300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ26025 (Selaginella moellendorffii), 3'ss of exon 3
gaagcgattaattcgtatcgagagttgataattgatcagattgctaatcaactagtagcagcaat-gatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
|| || || || ||| | | | | |||| | || | ||| |||||||||| || |||||||| |||||||||||||| ||||| | || || |||||||||| ||| | | |||| || |||| || ||||
-----------------------------gtatgctcgcatggcgaattttttttttctcttagttgatggtttgatctttgaatccaa----------agAGGAGGTATGGATGCCGGGCTATGATGCTGGAGACTGTGGCTGGAGTTCCCGGGATGGTGGGTGGCATGCTCTTGCACTGCAAATCCTTGCGCCGATTCG
upper sequence: LOC_Os02g21300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35306 (Selaginella moellendorffii), 3'ss of exon 2
--------gaagcgatta---------attcgtatcgagagttgataattgatcagattgctaatcaactagtagcagcaatgatg-----aatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGT--GCCGGGCGATGATGCTGGAGACGGTG--------GCGGCGGTGCCGGGGATGGTGGCCGGCG-----CGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG-----
|| ||| || ||| || || |||| | || ||| | | || | | ||| ||||| || | ||| ||| | ||| | || || | | | || | ||| || ||| | || || | || | || ||| ||||| || | | | ||| |
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctctctttctatcctttgaatatgaatgagcatgtttatgttgaatccttgcgaagctcctggggatcaaacgagtttttagtttgctagTCTTATAAACTTGGACTGGTTTTATTTTTGCAGCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGA
upper sequence: LOC_Os02g21300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ14430 (Selaginella moellendorffii), 3'ss of exon 2
gaagcgattaattcgtatcgagagttgataattgatcagattgctaatcaactagtagcagcaatgatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
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-----------------------------gtatgctcgcatggcgaa--attttttttttctcttagttgatgg--tttgatctttgaatccaa----agAGGAGGTACGGATGCCGGGCTATGATGCTGGAGACTGTGGCTGGAGTTCCCGGGATGGTGGGTGGCATGCTCTTGCACTGCAAATCCTTGCGCCGATTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcaactagtagcagcaatgatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
aatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagcgattaattcgtatcgagagttgataattgatcagattgctaatcaactagtagcagcaatgatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - -tgctaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgg