Sequence
atgc intronic sequence ATGC exonic sequencegtattattttgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40030.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G133226_T06 (Zea mays), 3'ss of exon 6
--------------------gtattattttgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcat-tcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT
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gtatcattttgattgcccttttttcttcttgaacactattttgattgctcttaacttcagatcaaacttcttatgtcttaaaatcttatatcct----gtttggatttcagGACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGGT
upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 6
gtattattttgatgacctgtttca---------------tattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT
|||||||| |||| || ||| | || || | || ||| | | |||| || | ||| | | | |||||| |||| ||||||||||| ||||||||||| || |||| || |||||||||||||| |||| | | || |||||||| ||||| |||| | ||||||||||
gtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagat-cttatacccctcttctggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG--
upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 6
--------------------gtattattttgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcat-tcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT
| | | |||| || ||| || | | | ||||| |||| | || |||| || | ||||||| |||||||| |||||||||||||||| ||||||||||| || |||||||||||||||||||||| |||| ||| || |||||||| ||||| |||||||||||||| |
gtatcattttgattgcccttttttcttcttgaacactattttgattgctcttaacttcagatcaaacttcttatgtcttaaaatcttatatcct----gtttggatttcagGACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccagattaaaccatatttgccttagcattcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT
tccattt CT-rich tract
attaaaccatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattttgatgacctgtttcatattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG