Sequence
atgc intronic sequence ATGC exonic sequence...tacatgttactaacacgcgcacatctgaattctcttctgcaggagcaggtctctgtaaatttagatgcattaccaaccttggatatgttttgaattgcagGGTTGGATCAGTAGTTTAATGATCTCACCTACATGCTGAGGAGTGAGGAGCTAGAAATGTATTGCTGACGCCAAATGGATGTAGAAATGCATACCAAGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g31440.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g31440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G871936_T03 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------tacatgttactaacacgcgcacatctgaattctcttctgcaggagcaggtctctgtaaatttagatgcattaccaaccttggatatgttttgaattgcagGGTTGGATCAGTAGTTTAATGATCTCACCTACATGCTGAGGAGTGAGGAGCTAGAAATGTATTGCTGACGCCAAATGGATGTAGAAATGCATACCAAGAT
|| | ||||||||||| ||| | | || |||||||||||||||| | ||| |||||||| |||| |||||||||||||||||||||||||||| | ||| ||| ||| | || | | | | ||||| || || ||
gtccggttgcactgctgtggtattgctgagtctgtattttaataatcgttgtgcatagaattcgttgggtttttataagttactaacac-cgcctacttcaactctcttctgcagGAGCCAGCCTCAGTAAATTTTGATGTATTACCAACCTTGGATATGTTTTGAATTTCGGGGCTGG-TCATCAATTCA----TTCCTTCAACATGTTGCAGAAGCAG-----------------------------------------------------
upper sequence: LOC_Os07g31440.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G871936_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------tacatgttactaacacgcgcacatctgaattctcttctgcaggagcaggtctctgtaaatttagatgcattaccaaccttggatatgttttgaattgcagGGTTGGATCAGTAGTTTAATGATCTCACCTACATGCTGAGGAGTGAGGAGCTAGAAATGTATTGCTGACGCCAAATGGATGTAGAAATGCATACCAAGAT
|| | ||||||||||| ||| | | || |||||||||||||||| | ||| |||||||| |||| |||||||||||||||||||||||||||| | ||| ||| ||| | || | | | | ||||| || || ||
ctgtggtattgctgagtctgtattttaataatcgttgtgcatagaattcgttgggtttttataagttactaacac-cgcctacttcaactctcttctgcagGAGCCAGCCTCAGTAAATTTTGATGTATTACCAACCTTGGATATGTTTTGAATTTCGGGGCTGG-TCATCAATTCA----TTCCTTCAACATGTTGCAGAAGCAG----------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggtctctgtaaatttagatgcattaccaaccttggatatgttttgaattgcagGGTTGGATCAGTAGTTTAATGATCTCACCTACATGCTGAGGAGTGAGGAGCTAGAAATGTATTGCTGACGCCAAATGGATGTAGAAATGCATACCAAGAT
atatgttttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatgttactaacacgcgcacatctgaattctcttctgcaggagcaggtctctgtaaatttagatgcattaccaaccttggatatgttttgaattgcagGGTTGGATCAGTAGTTTAATGATCTCACCTACATGCTGAGGAGTGAGGAGCTAGAAATGTATTGCTGACGCCAAATGGATGTAGAAATGCATACCAAGAT
-acatgtt
- - - - actaaca
- - - - - - - - - gcacatc
- - - - - - - - - - - - - - - - -cttctgc
- - - - - - - - - - - - - - - - - - - - -ggagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatt