Sequence
atgc intronic sequence ATGC exonic sequencegttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g26610.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
-gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctg--aataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
| ||| | | |||| || | | || || || | | | | | || ||| | | | | || |||||||| |||||||||||||||||||||| || |||||||||||||| |||||||| ||||||||||| |||||||| |||||||| ||||| ||||||
tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
--gttagtttgtactga-ttgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttc----agAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
| | | | | || |||| | || || || ||||| ||||| | | | || | | | | || |||| || | ||||| ||||||| |||||||||||||| || || ||||| ||||| |||||||| || || || ||||| ||||| |||||||||||||| || |||
gaagcattctaaatcaaattatata-tatagtttacttttgaattt--catatttttacaatataagtaca-tatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
gttagtttgtactgattgtata-attcaga-ttgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttc----agAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
| |||| | || | |||| || | | || || ||||| | | ||||||| | | | |||||| | | || |||| || | ||||| |||||||||||||||||||||| || || ||||| ||||| |||||||| || || || ||||| ||||| |||||||| ||||| || |||
-cttgtttcttctatatatatatatatatacttacttttgaatttcatat-tttcaccatg-taagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 13
----gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcc-tggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
| | | | | |||| | | | || | | || |||| ||| |||| | | | ||| | | | | | || |||||| || ||||||||||||||||| | ||||| || || |||||||||||||| || || |||||||||||||| |||||||||||||| || |||
tataaacaatct-tcttccttgtcacactttggttactattctgcattttgggtttccactg-ctgagaatattttaactgaagcagtaatgttgctgacagAATTCTGTTGGTGAGGAGTCACATCTGGCTATTGAGACTAGTGGCCATGGAGCTCTCAAGGAGAATCACTGGCTTGATGATGGTGCATACCTCATG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 13
---gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
|| | | | | | | ||||| || | ||| | | | | | | | | | | | | | ||||| || |||| || ||| | ||||| ||||| ||||| ||||| ||||| || ||||| |||||||||||| | || |||||||||||| | |||
taggtcgggtctaatgtagctaaagacctgaattgtgttagactttccttttatgctttttatcaccgggactctctgctgattgtcattcgtggaacagAACACGGTTGGAGAAGAGACTCATTTGGCTATCGAAACCAGTGGACATGGTGCCCTGAAGGAGAATCACTGGTTGGACGATGGTGCATATTTGATG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ24972 (Selaginella moellendorffii), 3'ss of exon 11
gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
|| ||| | || | | ||| || | | || | | | | || |||| | | ||||||||||| ||| |||| || || || || || || |||||| ||||||| |||| |||||| ||||||||||| ||| | |||
-------------------------------gtaatgacaaa-gtcatgtcacaca-aact---ttcagctcaactaacgcaaaatgg---ttgtagAACTCGGTGGGTGAGGAGTCCCATCTAGCCATTGAGACGAGCGGGCACGGAGCATTGAAAGAAAATCGCTGGCTGGATGATGGTGCTTATTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
tctttc CT-rich tract
tgaataaaatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttgtactgattgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttcagAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA