Sequence
atgc intronic sequence ATGC exonic sequence...agcaaaacaaaaccaactttttgataatttttacacattggcttgtaaattaaattattgatgtcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g02710.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G006069_T02 (Zea mays), 3'ss of exon 2
agcaaaacaaaaccaactttttgataatttttacacattggcttgtaaattaaattattgatgtcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
| | || ||| |||| || | ||| ||| | |||||||||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||||||| || |||||| |||| || ||||||| || || |||||||| ||| | |
aagataataaacatgtattttcattagtatttgtgtgttgattagtaaattaaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT
upper sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------agcaaaacaaaaccaactttttgata-atttttacacattggcttgta------aattaaatta--ttgatg--tcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
| | | | || || | | | | ||| | ||||| |||| | ||| | | ||| | ||| | |||||||||| | ||| ||||||||||||| |||||||||||||| |||||||| || || | ||| |||| |||| | | | ||| || | || | | | | | | |||| |
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttattctggtttttttgacagat-gattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
upper sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G42320.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------agcaaa---acaaaaccaactttttgat--aatttttacacattggcttgtaaattaaatt-----attgatgt-------cttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
| ||| ||||| || || || | || || || | | | || || | || || || | | | | || |||||||||| | ||| || ||||||||| ||||| |||||||| |||||||||||||| |||||| |||| || | | | ||||||| ||| | | | | | | | |
gtaagttcccttcacagctctgtctaagctattcacaggaatatcaaataaattgacaaatcccgtcttctggtttaacttgta-atacttttttataggtgaagtttcttcatagttttggtaatacctgtttttttgacagat-gattccttttcttccagACTTTTGGTCAGCATGGGAGAGAGCTTATCACCTCTGAACTTGCTTTTCGGATTTTGTCAATTTTGAGCGAAGAACAGTTCTTACCAAATAAAAACGGAG
upper sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0122g01410.t01 (Vitis vinifera), 3'ss of exon 3
agcaaaacaaaaccaactttttgataatttttacacattggcttgtaaatt--aaattattgatgtcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
|| | | | | || | ||||| | | ||| | | | || | ||| | | || | |||||||||| | ||| ||||||||||||| |||||||||||||| || ||||| || || |||||| ||||||| |||| | | |||| || | | | | | | ||||
agtactttgcaggccttatcttca-aatttacatgtagtggatagaatatctcagattggtatttgctggtttttttgacagat-gattccttgtcttccagAGTTTTGGGCAGCATGGGAGGGAGCTCATTACATCTGAACTTGCATTGCGGGTCCTATCAGTGTTGAGTGAAGAACAGTTTCTACCCAACATGGATCCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaattaaattattgatgtcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
ttttgac putative branch site (score: 3)
ttgtcttcc putative PPT
taaattattgatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcaaaacaaaaccaactttttgataatttttacacattggcttgtaaattaaattattgatgtcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC