Sequence
atgc intronic sequence ATGC exonic sequence...gactccaggaaaattatgtcccagaatcatcaatttggtagcagttgatgaaaaatgttcaggtggtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g35730.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G011169_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------------gactccaggaaa-attatgtc-ccagaatcatcaat-ttggtagcagttgatga-aaaatgttcaggtggtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
|| | | | ||||| | |||||| || | ||||| ||| |||| || || || ||||| || | ||| | ||||||||||||||||| |||||||| || ||||| | |||| | ||||| |||| | || ||||||||| ||||||| |||||||| |||| |||||||||
gtaagttcttccataggtcaaaacttatgataagacacaattttctattaaaaaaccaagattttttaagctagttaaccttgaatacacattataacaccagaagaattgtcaccaacattagttgctgataaaagatttagatgtctattgttact--------tttttctgtttgcagTCTGATTGCTTTTACAATGCCGGGTGGACGGCAGATATGCGTGAAGTTGTTAGTTTCCTTCATCAAGAGTATCCTAAGGCTCCACTATTCACTGTTGGGA
upper sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G35910.1 (Glycine max), 3'ss of exon 4
gactccaggaaaattatgtcccagaatcat-caatttggtagcagttgatgaaaaatgttcaggtggtactt--gttcctcaacctagtatttattc--ttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
|||| ||| || ||| | || || | ||| | | || || | || || ||| | ||| | | || ||||||||||| |||||||||||||||||||| || ||| |||| | || ||||| || || | || | ||| ||| || || |||| ||||||||
-----taggattattgtgcatattaatactgtgatcctgttgtggtttaatggttttcttgttttgttcctctagtaatgcaatttctcattaaaaccatttcagTCTGATTGTTTCTACAATGCTGGATGGACTGAGGATGTCCGCACAGTGGTTAATTATCTACACAAAGAGAACCCAAGGGCACCTTTGTTTGTTGTTGGGA
upper sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G31690.1 (Glycine max), 3'ss of exon 4
gactccaggaaaattatgtcccagaatcat-caatttggtagcagttgatgaaaaatgttcaggtggtactt--gttcctcaacctagtattta--ttcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
|||| ||| || | ||| | || || ||| | | | || | | || || ||| | ||| | | || ||||||||||| |||||||||||||||||||| || ||| |||| | || ||||| || || | || | || ||| || || |||| ||||||||
-----taggattattgtgcatctcaatactgtgatcctgttctggtttaatagttttcttgttttcttcctctagtaatgcaatttctcattaaaataatttcagTCTGATTGTTTCTACAATGCTGGATGGACTGAGGATGTCCGCACAGTGGTTAATTATCTACACAAAGAGAACCCCAGGGCACCTTTGTTTGTTGTTGGGA
upper sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G34340.1 (Arabidopsis thaliana), 3'ss of exon 5
--gactccaggaaaattatgtcccagaatcatcaatttggtagcagttgatgaaaaatgttcaggtg-gtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
|| | | | ||||| | | || ||| | | || | | || ||| | ||| |||| | || ||| | |||| ||||||||||| ||||||||||||||||| ||| | | | || | |||| ||||| || || || || |||||| | |||||| |||| |
gtgagttcgctagttttatgaatcta---cgaaaagttgtgattacttatatacatatattcttttatgtaagtgttgttttgtggcaaatgtat----gtagTCAGATTGCTTCTATAATGCTGGATGGACAGATGATATAAGGGTAGTTCTTGATTATCTTCAACACAAATACCCGAGGGCTCCTCTCTTTGCTATTGGCA
upper sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0035g00850.t01 (Vitis vinifera), 3'ss of exon 5
-gactccag--gaaaattatgtcccagaatcat---caatttggtagcagttgatgaaaaatgttcaggtggtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
|| || | | | ||| | || || | ||| | ||||| | ||| || ||| | ||| || | | || || ||||||||||||| | |||||||||||||||||||| ||| | | | ||||| || | |||||| |||||||| ||||||| ||||||||||||| |
agatgttagatggagttcttgtatgtggattatgttccttttcagaattcttgattataaaattt---atggaagatgtctctg---ttgttcattgtttgggcagTCTGATTGCATGTACAATGCTGGATGGACAGAGGATATAAGGAAAATTGTTGATCATCTTCATTGTCAGTATCCAGAGGCTCCTCTATTTGCTGTTGGAA
upper sequence: LOC_Os05g35730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0076g00210.t01 (Vitis vinifera), 3'ss of exon 5
gactccaggaaaattatgtcccagaatcatcaatttggtagcagttgatgaaaaatgttcaggtggta----cttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
| || | | | | | |||| ||||| || | || ||||| || | ||| | | | || | | | |||||||||||||||| || ||||||||||||||||| || | || || | | | | || ||||| | || ||| |||||| | ||||||||||| |
---tatagctagcattttgttagaatttgtcaaattggt-gctttgagcaaattatgtttgtgttcttaaactttgcagttatgctttgttataaattgtgcagTCTGATTGCTTTTATAATGCTGGATGGACAGAGGACATACGGGAAGTCATTGCTCATCTCCATCACGAATACCCAGTGGCTCCCCTCTTTGCTGTTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgaaaaatgttcaggtggtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
agttgat putative branch site (score: 5)
tttattctt putative PPT
tagtatttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactccaggaaaattatgtcccagaatcatcaatttggtagcagttgatgaaaaatgttcaggtggtacttgttcctcaacctagtatttattcttgcagTCTGATTGCTTCTACAATGCTGGATGGACAGAAGATTTCCGTGAGATTGTCAATTACCTTCATCAGAAGTATCCACAGGCTCCATTATTTGCTGTTGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT