Sequence
atgc intronic sequence ATGC exonic sequencegtgccttgcccttccctcttgttgaatccggctacctcctaccatacatactatatactcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g21900.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G885392_T01 (Zea mays), 3'ss of exon 1
gtgccttgcccttccctcttgttgaatccggctac-ctcctaccatacatactatatactcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
| | | || | | | | | ||| | || | || | || | | | | | ||| | | | |||||||| || ||||| ||||| || || |||||||||| |||||| ||||||||||||||||| ||||||||||| |||||||| ||||||||||
-----------------------gcacgcacgcacgcacgcgtcgt-tgaatgatagagtcccgccgcatgcgtttcgctcgctggcgttttcatgcgtggtgtttgtgttgtgtgtagGCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAA
upper sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------gtgccttgccc--ttccctcttgttgaatccggctacctcct-accatacatactatata--ctcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
|| ||| | |||| | | | || | | ||| || | | | | | || | | || | | ||||| || | | |||| | ||| |||| || ||||| || ||||| || || || || || | ||| ||||| |||||||| || || ||||||||||||||||||||||| |||||||
gtatgccaccccccccccccccccccccccaccagaagttttaaattttttctgatgtcttaatagacttatatatgttacgtgtgatcaactgatgatcatgcagaaaacagaaattaactttttgtgtatgtga-attttaatttttttgaggttttgttttttctattcaacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
upper sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 2
gtgccttgcccttccctcttgttgaatccggctacctcctaccatacatactatatactcacaagtcaattgagtcacaattta--acccga---ttagattcctcttttcctt-cttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
|| | | | | || ||| | | || | ||| | ||| | | ||| | ||| | | || || | || ||| || ||| |||| || ||||| || ||||| || || || || || | || ||||| |||||||| || || ||||||||||||||||||||||| |||||||
gtatatatgaccccagaagttttaaatttgcttctgagttattttttatatattttacgtgtgatcgatgtgaatttgaatatgttattggaatattgggttttgatttgttttgtttccacagGCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAA
upper sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgccttgcccttccctcttgttgaatccggctacctcctaccatacatactatatactcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
| | | | | | | ||| | | | | | | | | | | | ||| | || || ||| || || || || | || | || ||||| || || || || || || || || | ||| |||||||| || || ||| | ||||||||||||||||| |||||||||||||
--------------gtaaacgctacaataaaccatttttt-ttatagttgccaaaacatgatatat-atctaatcttcaag--agcctga--gaattgcttttgtcttttgattacagTCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAA
upper sequence: LOC_Os08g21900.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 2
gtgccttgcccttccctcttgttgaatccggctacctcctaccatacatactatatactcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
| | ||| | | ||| | | | | | | | | | ||| ||| || |||| | | |||| | ||| | |||||||| || ||||| || || || || |||| || || ||||||||||| || || ||||||||||||||||||||||| |||||||
--------------ctttagagcaaatttgcagctccactattttgtgtggggtgtgtttgtgt-ttattctcattacattttgttgtaat---attctttccatttttctgttgtagTCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
atttaac putative branch site (score: 3)
ttagattcctcttttc putative PPT
acaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgccttgcccttccctcttgttgaatccggctacctcctaccatacatactatatactcacaagtcaattgagtcacaatttaacccgattagattcctcttttccttcttctttagGCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA