Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttctagtttatattcaaatcccggtgcattgcgttttataaattgaaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g09740.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 14
gtatgct-tctagtttatattcaaatcccggtgcattgcgttttataaattg-----aaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA
||||| ||||| || ||| ||| ||| ||| | | | || || | | |||| |||| |||| |||||||||| |||||||| |||||||| ||||||||| |||||||||| || || ||||||||||| ||||| ||||||| |||||| |||||||||||||| |||
gtatgtgatctagattgtatccaa-tcctggttcgcttcagcttcgaagtggttgttgaaatagcctttggatgatcattgcagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv10s0116g00100.t01 (Vitis vinifera), 3'ss of exon 14
--------------------------------------------gtatgcttctagtttatattcaaatcccggtgcattgcgttttataaattgaaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA
| | || || || | |||| | ||||| |||| | || | | ||||| | | || ||||| |||| |||||||||||| || ||||| ||||||||||||| || ||||||||||| ||||| || || || ||||| ||||| | |||||||
gtagaacatgtgctacattgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctcttgacattg-gtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv10s0116g00050.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------gtatgcttctagtttatattcaaatcccggtgcattgcgttttataaattgaaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA
| | || || || | |||| | | ||||| |||| | || | | ||||| | | || ||||| |||| |||||||||||| || ||||| ||||||||||||| || ||||||||||| ||||| || || || ||||| ||||| | |||||||
gtagaacatgtgctacattgctgaacacccatttttgtgttcttgaaatattttatagcattctttaatctctggacattg-gtttgtttctatggttctcatcttcttttttgtgttttagTTCAAGAGTGAGATCAGAACAGTCACTTGTGAGATGGGCTACTCCCCAACTTCATGATATAGATGCCCTGGCAAAAATGGTTGATCCTTCCCTAAATGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcccggtgcattgcgttttataaattgaaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA
ttctgat putative branch site (score: 3)
ttttataaattgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttctagtttatattcaaatcccggtgcattgcgttttataaattgaaaatgaccttctgatggatattgcagTTCTAGAGAGAGATCAGAACAATCTCTTGTTCGATGGGCTACTCCACAGCTTCATGATATCGATGCGCTTGCTAAGATGGTGGATCCAGCATTAAATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA