Sequence
atgc intronic sequence ATGC exonic sequencegtaactcctttgtttacttattaagcagttatccatgtctgcaagagtaatgtttctatgcttatagtcaaccaatatatgactatgcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G017845_T02 (Zea mays), 3'ss of exon 4
gtaactcctttgtttacttattaagcagttatccatgtctgcaagagtaatgtttctatgcttatagtcaaccaatatatgactatgcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
|||||| ||||||||||| || ||||||| ||| | ||| || |||| || || | |||||||||||||||| || || ||||||||||||||||| ||||||||||||| |||||||| |||||||||||||||||||| ||
gtaacttttttgtttactt-tttagcagtt-------tctttcaatgtactgac------cttaaagccatgc------------tgcagTTCTCCATGTCCGGGAATCATCCATACCATAAAACTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTC
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 5
gtaactcctttgtttacttattaagcagttatccatgtctgcaagagtaatgttt---ctatgcttatag--tcaaccaatatatg--actat-gcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
|| | || | || | | ||| | || | | ||| || | |||| | | ||| || | ||| |||||| |||| || || || | || || |||||| ||||||| ||||| ||| || ||||||||||||||||||||||| ||
---------gtgctaacattaccggccacattgcttgttttcatatatggtttttattctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 4
--gtaactcctttgtttacttattaagcagttatccatgtctgcaag-agtaatgtttctatgcttatagtcaacca----atatatgactat-gcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT-
|||| || || ||| || | | | || || | |||| | |||| | | | |||| | ||| ||||||||||| || || || | || ||||||||| ||||||| ||||| ||| || ||||||||||||||||||||||| ||
tgctaacattactggcaac--attgcttgttttcctgttttcataaatggtttttattctgtacttacacttttgttttatacatattattattgcagtTCTCCACATCTGGGAATTACCCTTACCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTCG
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 5
-------gtaactcctttgtttacttattaagcagttatccatgtct-gcaagagtaatgtttctatgcttatagtcaaccaatata--tgactatgcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
|| || | || | ||| || | | | || | | | ||||||||| | | || |||| || || ||| || ||| || || | || || || ||| | ||||||||||||| || |||||||||||||||||| |||||||| |||
gtaatcagtggctattgtgctatctttatagattgctgcagaagtatcatttgtttgatgtttctactggctaacttgacatatattcttgttcttgtagTATTCTATGAATGGGAATTACCCTTATCACAAATCTTGCTACAAGGAGCACTATCACCCAAAATGTGATGTTTGCAAGCACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctgcaagagtaatgtttctatgcttatagtcaaccaatatatgactatgcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
aatatatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactcctttgtttacttattaagcagttatccatgtctgcaagagtaatgtttctatgcttatagtcaaccaatatatgactatgcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA