Sequence
atgc intronic sequence ATGC exonic sequence...ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g42320.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 2
------ttttgtgtagt-tac-tgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
|| | |||| | ||| || ||| | || | | || | | || | || ||| | | ||| || ||||||| ||| || |||||||||||||| || |||||||| || ||||||||||||||| ||||||||||||| || ||||||||||||
gctgtgttctatgtaatatacatggtcattggtta--ggcagtacaaccattttattttacttgtg--catctttgttaattctgaaatat----gtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
ttttgtgt-agttactgctcag--agactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
| | ||| | | | | | | | || | | || | || ||||| || || || || | | | || ||| |||||||||||||| || |||||||| || ||||| ||||||||| |||||||||||||||| ||||||||||||
tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttatttta--cttgtgcatct-ttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G824831_T04 (Zea mays), 3'ss of exon 3
------ttttgtgtagt-tac-tgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
|| | |||| | ||| || || | || | | || | | || || ||| | | ||| || |||| || ||||| |||||||||||||| ||||||||||| || |||||||||||||| |||||||||||||||| ||||||||||||
ataatgttctatgtaatatacatggtccttggtta--ggcagtacaaccattttgttttacttctgcctc--tttgttaattccgaaatatatc----atgtttgcagCTGCCAATGGTGTAGTCATTGCCACTGAGAAGAAGCTGCCTTCTATTTTAGTGGATGAAACATCT
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
-ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttccct--tttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
| | ||| || | | | ||| ||| | || | | | | | || | | | ||| | | | ||| | || ||||||||||| ||||| || || || ||||| |||||||||||||| ||||| || || |||||||||||
actctctgtgctt--cgttgggttctcgtgtcttgtagatggt-ttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
----ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
| | ||| ||| | | | ||| ||| || | ||| | | | | || | | | | | || | || |||||||||| ||||| || || || || || |||||||||||||| ||||| || || |||||||||||
tttactctctgtggtt--cattgggttcttgtgtcttgtagatga--tttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
upper sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 2
ttttgtgtagt-tactgctcagagactacagtctg--ttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgt-tatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
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---aatgtggcataatggttttgatttgttctcaaatttggtcatatttggagttcatcttgtcccatt-accaattgactaatacttttgcctgttactgcagCTGCCAATGGTGTTGTTATTGCAACTGAGAAGAAACTACCTTCTATCTTGGTGGATGAGGCATCGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|27578244|gb|CB000939.1|CB000939EST: GCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG CTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAG
genomic: GCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAGgtgcgtcccg ... atgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAG
EST:
gi|88288359|gb|CI661564.1|CI661564EST: GCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAG CTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAG
genomic: GCACGCGCTCACCGCGGTCGGATCCGGCCAGACGTCCCTCGGGATCAAAGgtgcgtcccg ... atgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
tattgat putative branch site (score: 3)
tatatttgttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - ttactgc
- - - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg