Sequence
atgc intronic sequence ATGC exonic sequence...tgaagcacatttgtcctgaaaacagtaatgtaatagtttacagaagcagttattacacatataaactgattgatcagcgttttctattctgtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCAGATATGAGAACAGGGATAGAGGCTGCCGAGTATGGTGCTGAGCTACAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g34210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G091560_T01 (Zea mays), 3'ss of exon 1
-tgaagcacatttgtcctgaaaacagtaatgtaatagttta-cagaagcagttattacacatataaactgattgatcagcgttttctattctgtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCAGATATGAGAACAGGGATAGAGGCTGCCGAGTATGGTGCTGAGCTACAGA
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gggaaatccagagggaatgaaaagaattacacagcgtctcatcacataaaagtacagcagcttcag--ttattgatcagtggttgctactttggctggttagGTTGACCTAAACAGGGCTGGCGTACCTTTGCTCGAAATTGTCTCAGAGCCAGACATGAGAACAGGGATAGAAGCTGCTGAGTATGGTGCTGAACTGCAAA
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ26002 (Selaginella moellendorffii), 3'ss of exon 1
tgaagcacatttgtcctgaaaacagtaatgtaatagtttacagaagcagttattacacatataaactg-attgatcagcgttttctattctgtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCAGATATGAGAACAGGGATAGAGGCTGCCGAGTATGGTGCTGAGCTACAGA
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-----------------------------gtaacgtttttcttctcttgttttttttttctttgctcgtgtttgtgagaag-----agtatgtgtttgtagGTGGATTTAAACAGGGCTGGAGTTCCTTTACTGGAGATTGTCTCGGAGCCGGACATGAGAACCGGCATTGAAGCTGCCGAGTACGCGGCGGAGGTGGCAA
upper sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ14409 (Selaginella moellendorffii), 3'ss of exon 1
tgaagcacatttgtcctgaaaacagtaatgtaatagtttacagaagcagttattacacatataaactgattgatcagcgttttctattctgtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCAGATATGAGAACAGGGATAGAGGCTGCCGAGTATGGTGCTGAGCTACAGA
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---------------------------------------------------------------------gtgagaagagatctcttatgtgtttgt--agGTGGATTTAAACAGGGCTGGAGTTCCTTTGCTGGAGATTGTCTCGGAGCCGGACATGAGAACCGGCATTGAAGCTGCCGAGTACGCGGCGGAGGTGGCAAMapped 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|33797712|gb|CF324715.1|CF324715EST: AAGAAGATGCTGGCAAGCTGCTTCACTCTGAATCCGGGAGTTACTCTCAG GTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCA
genomic: AAGAAGATGCTGGCAAGCTGCTTCACTCTGAATCCGGGAGTTACTCTCAGgttttccttg ... gtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCA
EST:
gi|38469413|gb|CF953544.1|CF953544EST: AAGAAGATGCTGGCAAGCTGCTTCACTCTGAATCCGGGAGTTACTCTCAG GTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCA
genomic: AAGAAGATGCTGGCAAGCTGCTTCACTCTGAATCCGGGAGTTACTCTCAGgttttccttg ... gtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagttattacacatataaactgattgatcagcgttttctattctgtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCAGATATGAGAACAGGGATAGAGGCTGCCGAGTATGGTGCTGAGCTACAGA
ttttctattctgttt CT-rich tract
tattacacatataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaagcacatttgtcctgaaaacagtaatgtaatagtttacagaagcagttattacacatataaactgattgatcagcgttttctattctgtttatctagGTTGACTTAAATAGGGCTGGCGTTCCTTTACTTGAAATTGTCTCAGAGCCAGATATGAGAACAGGGATAGAGGCTGCCGAGTATGGTGCTGAGCTACAGA
- - gcacatt
- - - - - -tgtcctg
- - - - - - - - - - - - - - - - - - - - cagaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - acacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg