Sequence
atgc intronic sequence ATGC exonic sequence...ctgcttctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacaccactttcttctcaacagGTGGTCAAACAAGCATCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g15040.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 5
-----------------------ctgcttctcta-tgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaattttt--ttttaacacca-ctttcttctcaacagGTGGTCAAACAAGCATCAG
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atgttttttgcattgtatagctgtagtgcgtatactacttgttcaattgcaaaaaaaaatcacagctaaagttttcagtgccatcatattaaactttcagTATTAACACCAACTTTCTTCTCGACAGGTGGTCAAACAAGCATCAG
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147726_T03 (Zea mays), 3'ss of exon 1
-------ctgctt-ctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacacca-ctttcttctcaacagGTGGTCAAACAAGCATCAG
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gcgtatactacttgttcaattgcaaaaaaaaatca--cagctaaagttttca-gtgccatcatattaaactttcag------tattaacaccaactttcttctcgacagGTGGTCAAACAAGCATCAG
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147726_T05 (Zea mays), 3'ss of exon 2
-------ctgctt-ctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacacca-ctttcttctcaacagGTGGTCAAACAAGCATCAG---------------------------------------------------------------------------------
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gcgtatactacttgttcaattgcaaaaaaaaatca--cagctaaagttttca-gtgccatcatattaaactttcag------tattaacaccaactttcttctcgacagGTGGTCAAACAAGCATCAGGTACCGGCTCTTTATCATGATAGTAAATTCCTGACTGTCATTTCTGAAGTAAATAATACTATTGCATTTATTTAATCACCGMapped 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|86478438|gb|CI121071.1|CI121071EST: AGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG GTGGTCAAACAAGCATCAG
genomic: AGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
EST:
gi|8956150|gb|BE229954.1|BE229954EST: GAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG GTGGTCAAACAAGCATCAG
genomic: GAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
EST:
gi|27554607|gb|CA998507.1|CA998507EST: TGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG GTGGTCAAACAAGCATCAA
genomic: TGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
EST:
gi|88383993|gb|CI631883.1|CI631883EST: CGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG GTGGTCAAACAAGCATCAG
genomic: CGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
EST:
gi|218486133|gb|FG956315.1|FG956315EST: CGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG GTGGTCAAACAAGCATCAG
genomic: CGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
EST:
gi|27554323|gb|CA998223.1|CA998223EST: TGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG GTGGTCAAACAAGCATCAG
genomic: TGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
63 (upstream exon),
37 (downstream exon)
Score:
31CGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttccttcactttaaaatatccaatttttttttaacaccactttcttctcaacagGTGGTCAAACAAGCATCAG
ttttaac putative branch site (score: 31)
caccactttcttctc CT-rich tract
ttcactttaaaatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcttctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacaccactttcttctcaacagGTGGTCAAACAAGCATCAG
-tgcttct
- - - - -tatgcta
- - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacca