Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatttgtgtgagaaacattgtatcgtcgtgcaaactcaaactttctgtgtgactgacactgctggacgcatgtttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g37990.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g37990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 9
------------------gtaaggatttgtgtgag--aaacattgtatcgtcgtgcaaactcaaactttctgtgtgactgacactgctggacgcatgtttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT-
|| || | || | | ||| ||| ||| | | ||| || | | || ||| | ||| || ||||||||||||||||||||||||| || ||||| || | ||| || |||||||| |||||||| |||| ||| | || | || | ||||| || |
tacaggcatattcactgtgtcagtagttatattttttaaatgttgggattatttgctagtttgaacaaactatatatcttaca-------aaacattacattttaggTTAGGAACACAAGGACTGTAAACCGAACTGGGCATCTAACTGGTTACAAGCTAGTACCTGGCTCAAATTGTTTACCTTTAGCTGGCTCAGAGGCTAAGTT
upper sequence: LOC_Os02g37990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 9
-------gtaaggatttgtgtgagaaacattgtatcgtcgtgcaaactcaaacttt----ctgtgtgactgacactgct-ggacgcatgt--ttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
|| | || | || || | | || || || |||| | | || | ||| | | || | || || ||||||||||||||||||| ||||| || ||||| || | |||||| |||||||| ||||||||||||| ||| | || |||| | ||||| || |
ttctgcagttatatttctcaaagctgagatggtttacttgttagaaaacactctttgacatattttaaccagcgtcgctcaaatgaatttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
upper sequence: LOC_Os02g37990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 9
-------------------gtaaggatttgtgtgag--aaacattgtatcgtcgtgcaaactcaaactttctgtgtgactgacactgctggacgcatgtttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
|| || | || | | ||| ||| ||| | | ||| || | | || ||| | || || ||||||||||||| ||||||||||| || ||||| || | ||| || |||||||| |||||||| |||| ||| | || | || | ||||| || |
ctacaggcatattcactgtgtcagtagttatattttttaaatgttgggattatttgctagtttgaacaaactatatatcttacaatatattacat-------tttagGTTAGGAACACTAGGACTGTAAACCGAACTGGGCATCTAACTGGTTACAAGCTAGTACCTGGCTCAAATTGTTTACCTTTAGCTGGCTCAGAGGCCAAGT
upper sequence: LOC_Os02g37990.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 9
-gtaaggatttg---tgtgagaaacattgtatcg-------tcgtgcaaactcaaacttt---ctgtgtgactgacactgctggacgcatgtttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
| || ||| |||| |||| || | || | || ||| ||| |||| | |||||| ||| | | | | ||||||||||||||||| ||||| || | |||||||| | |||||| |||||| | ||||||||||||| ||| | ||| | || ||||||| || |
aatgagcattaaaattgtgctaaactgggtcttaattaggctcatattaagtcatcttttggactgttttactgactctggataccatttcatattccagGTTAGGAACACAAGAACTGTCAACAGGACTGGACAGCTAACAGGCTACAAGTTAGTACCTGGTTCAAACTGCTTGCCATTAGCTGGTTCTGAGGCCAAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtgcaaactcaaactttctgtgtgactgacactgctggacgcatgtttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
gactgac putative branch site (score: 2)
tttgttc putative PPT
aaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatttgtgtgagaaacattgtatcgtcgtgcaaactcaaactttctgtgtgactgacactgctggacgcatgtttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG