Sequence
atgc intronic sequence ATGC exonic sequencegtaataaaaatgagtcttgaactgtttattttgtcagtccatcattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgcttttctcacaataataaggtcattgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g43750.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 5
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgctttt-ctcacaataataaggtc--attgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
||| | | | | | | || || | || | || | | ||| |||| ||||| ||| || || || ||| | | ||| ||| |||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||
------------------------------atgtggtttcttg--catatcatcattgctgcttgtttgc-actcaatgcttttgtatcatg-gattgtgtttactgactatgatatgcacgcattaattatagTTGAGAAGGCAAAATATATTTACATTGCTGGATTTTTCCTTACGGTATCCCCGGATTCTATTCAACTTGTTGCTGAGCATGCCGCTGCAACTAACAAG
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 7
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattg-tgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgcttttctcacaataataaggtcattgatt--gtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
|| | | ||| | || | |||| ||| | | | | | | || || ||| || || | || | | | || || ||||||| ||||| || ||| |||||| |||||||||||||||| ||||| || |||||||| ||| | |||||||| ||||| ||||||| |||||||
------------------------------------gtaccttgttgatattggttctgttt-ctatctcatatac---ctgaatattccagatgactgacatt-ttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAG
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 7
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgcttttctcacaataataaggtcattgatt--gtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
|| |||| | || | | || | | | ||||| ||| || || | || | | | || || ||||||| ||||| || ||| | |||||| |||||||||||||||| ||||| || |||||||| ||| | |||||||| ||||| ||||||| |||||||
-----------------------------------------gtatattgttgatattggctctctttctctctcatacctgaatatttcagatgactgacatt-ttgttattgtgtgtttgttttttcaatagTTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
gtaataaaaatgagtcttgaactgtttattttgtcagtccat-cattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattg-cttttctcacaataataaggtcattgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
| || | | || ||| | || | | | ||| ||||| | ||| || | | | |||| | || || | ||| | | | || | | | |||||| ||||| || |||||||| |||||||| ||||||||||| ||||| || |||||||| || || |||||||||||||||||||||| |||||||
------------------gtaccctgtcattggtctatgcaggctctcttttatttctgtctcc-----acttcatagctgac-taattcagtggactgacattttttattgtg-caattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 7
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattg-cttttctcacaataataaggtcattgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
|| ||| | | ||| | || || || | || |||||| | || | | || |||| | || || | ||| | | | || | | | |||||| ||||| || |||||||| ||||| |||||||||||||| ||||| || |||||||| || | |||||||||||| ||||||||| |||||||
-------------gtaccctgtcgttgttctatacaggctctcttttattt--ctctctccacttcata--------tctgagtaattcagtggactgacattttttattgtg-caattttttgtgacgcagTTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatgtgtttcatttgattgcttttctcacaataataaggtcattgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
acaataataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataaaaatgagtcttgaactgtttattttgtcagtccatcattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattgcttttctcacaataataaggtcattgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC