Sequence
atgc intronic sequence ATGC exonic sequence...tggatctgtgggtcactctttgctggttatatccttctaatactattgagttcacaacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g33210.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g33210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G149567_T01 (Zea mays), 3'ss of exon 9
tggatctgtgggtcactctttgctggttatatccttctaatactattgag---ttcacaacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA-
|||||| | | || || || ||| |||| | | | ||| || | || ||||||| ||| || || |||| |||||| ||||||| |||||||||||||||| || ||||||||| ||||||||||||||||| | |||||||||||||| || ||||||||||||||||||
-------gtgggttatgccttccttcttgcatcattctcgcgttctgaaaagacatgttgcatggatcat-gtcttgaaaaagttatttattcgattt-gcagGAA-TCAGCTATGATTAGGTTAGATATGAGCGAATATATGGAGAGGCATGCTGTGAGCAAGCTTATAGGCTCTCCTCCGGGGTACATGGGATTTGGTGAAG
upper sequence: LOC_Os04g33210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G149567_T02 (Zea mays), 3'ss of exon 5
tggatctgtgggtcactctttgctggttatatccttctaatactattgagttcacaacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA-
|| ||||||| ||| || || |||| |||||| ||||||| |||||||||||||||| || ||||||||| ||||||||||||||||| | |||||||||||||| || ||||||||||||||||||
--------------------------------------------------------------------gtcttgaaaaagttatttattcgattt-gcagGAA-TCAGCTATGATTAGGTTAGATATGAGCGAATATATGGAGAGGCATGCTGTGAGCAAGCTTATAGGCTCTCCTCCGGGGTACATGGGATTTGGTGAAG
upper sequence: LOC_Os04g33210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G51070.1 (Arabidopsis thaliana), 3'ss of exon 9
tggatctgtgggtcactctttgctggttatatccttctaata--ctattgagttcac--aacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA-
|| ||| | |||| | || ||| |||| | ||| ||| ||| | | | ||| | || | | |||||| | | | | || || || |||||||| || |||||||| ||| ||||||||||| |||||||||||||||| || || | || |||| |||
-----------gtacagcttcattaacaatatagtgctgataaatgattgtggtcattgaaccgattccttcatcccc----cgtttttcattggttattgcagGAAGA-ATCCATGCTGAGATTGGACATGAGTGAATACATGGAGCGTCATACTGTGAGCAAGCTGATAGGCTCTCCTCCTGGTTATGTTGGCTTTGAAGAAG
upper sequence: LOC_Os04g33210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv19s0014g00020.t01 (Vitis vinifera), 3'ss of exon 9
-tggatctgtgggtcactctttgctggttatatccttctaatactattgagttcacaacatatttcgttg--ttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA-
| || | | |||| || | | || | | | | |||||| || | | | ||| |||| | ||| || | | |||| | || || || || |||||||| |||||||||| |||| |||||| ||||||||||| ||||| ||||| || | || | ||| ||
ctaaattcttctttacagtgatgcttattgtcaatgatcagtagcag-gggcttccaacattggaatttaactctcatttctcttgattctgttattgca---gGAGGCAGCAATGGTAAGATTGGACATGAGTGAATATATGGAGCAGCATAGTGTGAGTAAGTTGATAGGATCTCCCCCAGGTTATGTAGGCTATGGAGAGG
upper sequence: LOC_Os04g33210.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ27469 (Selaginella moellendorffii), 3'ss of exon 9
tggatctgtgggtcactctttgctggttatatccttctaatactattgagttcacaacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA-
| | || | || || || | | | || | ||| || ||| ||||| | || | | ||||| |||||||| ||||| |||||||| ||| ||||||||||| | || || |||||||| ||||| | |||| ||| ||
-----------------------------------gtaagtcctttcatacgcatg-cacatat-ggcgccttaccacggtttttttcttc------cagGAGGAC-GCCATGATAAGGTTGGATATGAGCGAGTACATGGAGCGTCATACTGTGAGCAAGCTTATCGGTTCTCCTCCCGGATATGTTGGATATGGCGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagttcacaacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA
ttgcttctttcatttc CT-rich tract
ttttgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggatctgtgggtcactctttgctggttatatccttctaatactattgagttcacaacatatttcgttgttttgaaaatgttgcttctttcatttcacagGAAATCAGCTACTGTTAGGTTAGATATGAGTGAGTATATGGAGCGGCATGCTGTGAGCAAGTTGATAGGCTCTCCTCCAGGATACATGGGATTTGGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - caacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg