Sequence
atgc intronic sequence ATGC exonic sequence...aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G053644_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagata--aatgttatctgtttacttgatcaaaatatgttttcgatatttt-ctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
|| || | | | | | || | || | ||| | | || | || |||| | || |||| |||| | ||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||| ||| |||||||| ||| |||||||||||| ||||||||||||
gtatgttcccctatttttgcgacttatggtgatgtcccttgctgtctcggcaataaagtatcaccagactgcaggatttaggccgcccaggtccaattgtattgtaataaaaacttttaaactggtcagtttgtgtaattaaaac---tttttaacattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCATCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 8
aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatatttt-ctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
| | | || | ||| | | || ||| | | |||| | || |||| ||| | ||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||| ||| |||||||||||| ||||||||||||
-----------gtacgtcactattatgctgacagcgattccatacagattaattagctccagtttgtgtaattaaaa----cttttaacattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCAGCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
| ||| | || | ||||| || | | | |||| | ||| ||| | | || ||| | | | | |||||| | |||||| || ||||||||||| ||||||||||| |||| ||||||||||| ||||| || |||| || |||||| ||| | || || |||||||||||
-gtatgtgctttttggtt--cacttagctg-cagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgt--gctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
aggatgaggaagatgatgagtacttaattgatgctcttacagtaata--gataaatgttatctgtttacttgatcaaaatatgtt---ttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
| || ||| | | | | | | | | || ||| ||| | || || | || || | | | | | || | ||||||||| ||||||||||| ||||||||||| |||| |||||||||||| ||||| || |||| || || ||| ||| | || || |||||||||||
---------------gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtattttgcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
| | | ||| | || |||| | | | | || | | ||| | | ||||| || || | ||| ||| ||||| |||||||| |||||||||||||| ||||| ||||||||||| |||| || | || || ||| || | | | || || || ||| ||||
--------gtaagttctgatttattcattggaacagtagcctagctcctta--cggtgcaccattatctcactgaaataagtctt---tctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 9
aggatgaggaaga-tgatgagtacttaattga--tgctcttacagtaatagataaatgtt--atctgtttacttgatcaaaata-tgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
| ||| | | || | | || |||| | | | |||| || ||| | | |||| |||| | || ||| | ||||| |||||||| |||| |||||| |||||||||||||||| ||||||||||| || || || |||| || |||||| || | || || ||||| ||||||
-gtatgttgttcactggtttatgtatatttgagctatcgtgtaaataatttatgcatgcttgaattgttactaatatcacagtactgtatcttgtattt---gtagTGAGAGTGCAACTGAATATACAGATGATGAGGATGTCAGCTGGAAAGTTCGAAGAGCAGCAGCTAAATGCTTAGCAGCTTTGATTGTTTCTCGACCTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
acttgat putative branch site (score: 5)
tattttctcc putative PPT
aaaatatgttttcgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - atgatga
- - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatcaaa