Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g25310.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactc-cagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
| ||| | | || ||| | | | | || |||| | ||| |||| || || ||||| ||||||||||| || |||||||| |||||||| |||||||| ||||||||||||||||||||||| ||||| ||||| || ||||| ||||||||||
--gtaagat-tctatcagaggtccagaacattatagccttagagggttgacttta-tttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
gtaa--aggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactc-cagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
|||| | || | | | || | | | | || |||||||| ||| |||| || || ||||| || |||||||| || |||||||| |||||||| ||||||||||||||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||
gtaagtaagactactactagaagtcgagaacattgtagccttagagttctcacttca-tttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctga--ttactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
| | ||| | ||| | || | | || | | || | || |||||||||| | | ||| | ||||| ||||||| |||||||||||||||||| ||||| |||||||| || |||||||||||||| || || || ||||| ||||| || || ||||| || |
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctct-ttaatttgcttttgcatattactaagacacttgttac----atttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G07280.1 (Glycine max), 3'ss of exon 8
-----------------------------------------------------gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcac-ttcaatttttgtttctga--ttactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
||| | |||| |||| || | | || | | | || || ||||||||| | | ||| | ||||| ||||||| || |||||||||||||| ||||| |||||||| || ||||| |||||||| || || || ||||| ||||| || || ||||| || |
gtaatttcccaagttacagttgtatgcatgacatttttcctttttaatttcctttaactgctctta---aatctgtttttgcatattactaagccactcgttacattttttttttgttttttaacttagtacagGTTGATGAGAAAGGTATGCGCTGGTTTTATACTGGTGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G07060.1 (Glycine max), 3'ss of exon 8
-------------------------gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttc-aatttttg------------tttctga--ttactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
| | |||||| || | | | || | | | || || | | | | ||| | || ||| ||| ||| | ||||| |||||| || ||||| |||||||| ||||| ||||| || || |||||||||||||| || || || ||||| ||||| || |||||||| || |
gtaattttcaaactttcagttatatgcctattatctttcccttttaactttcttcaactgctctaaaatgtacctttgctaatgtatgccacatgggtcatttttgaacttagtacagGTTGATGAGCATGGTATGCGTTGGTTTTATACTGGGGATATCGGACAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAGGATATTGTCA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------------------------------gtaaaggatctttgccaatcatcct-tggtggtcaaatacaatatttt--tcacttcaatttttgtttctgat-tactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
|| | || | | || | | ||| | | ||| | | | || | | | | | | | || ||||| ||||||||||| |||||||||||||| ||||| || ||||| ||||| || ||| |||| ||||| || || ||||| || || |||||||| || |
gtaataagtaacttcttttgtggataggtgcctgtattggcatttgtatttactttttgtgtatttatatatatatatatgtgtgtgtatgtatatatacatacacaatacatatatactttcttatagtgcaacacttcaacttgtgaatagctgcgttggtgacatatcgtctgctacagGTTGATGAGAGGGGCATGCGCTGGTTTTATACTGGTGACATTGGACAGTTTCAACCTAATGGTTGCCTTGAAATAATTGACAGGAAGAAGGATATTGTTA
upper sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8
gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
| | | | | | | | | | | | || ||||| || ||| |||| || |||||||| ||| | ||||| |||||||| || ||||| ||||||||||| ||||| ||||| || || | || | || ||||| || || |
-------------gtacaacttttcagtttccttgaagcgttcatgcttaattgggttttt--ttgtga-------agGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
ttctgat putative branch site (score: 3)
ttactcc CT-rich tract
aaatacaatatttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactccagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA