Sequence
atgc intronic sequence ATGC exonic sequence...ttttttttttaccgtagggggtagcttattagttgcatcttattttataaacaagagtaagattagtgcacaaatatattcaaacctcttcaacttgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACATCTCAGCTGTGAAGAGCCCCCAACAGGCCATTGGTGCTGCTATCAAGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g53750.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g53750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G171998_T01 (Zea mays), 3'ss of exon 4
ttttttttttaccgtagggggtagcttattagttgcatcttattttataaacaagagtaagattagtgcacaaa---tatattcaaacctcttcaacttgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACATCTCAGCTGTGAAGAGCCCCCAACAGGCCATTGGTGCTGCTATCAAGCA
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-gtaaccttgcatgtatatcactacatttttat-gcat-ttgctttcgaaacaagtacacgatttgttcacaaaatatgtgtcacagcctcttccacttgcagGTTGGATATGCTATGCTGAAAAGACTCTTGGTTCATACATACTACCTTACATATCATCTGTAAAGAGCCCACAACAGGCAATTGGTGCAGCCATTAAGCA
upper sequence: LOC_Os03g53750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G456690_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------ttttttttttaccgtagggggtagc--ttattagttgcat-cttattttataaacaagagtaagattagtgcacaaa-tatattcaaacctcttcaacttgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACATCTCAGCTGTGAAGAGCCCCCAACAGGCCATTGGTGCTGCTATCAAGCA
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gtaagatttttgctgggaacatgacatgtggatacttgcataacgcagtttgggttttaaaaattctgtaaccttgcatgcataatactaatggtttacaactaccttttatgcatttgctttagaaacaagtgcatgatttgttcacaaaatgtgtcacagcctcttccacttgcagGTTGGATATGCTATGCTGAAAAGACTCTTGGTTCATACATCCTACCTTACATCTCATCTGTGAAGAGCCCGCAACAGGCAATTGGTGCAGCCATTAAGCA
upper sequence: LOC_Os03g53750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0508g00020.t01 (Vitis vinifera), 3'ss of exon 4
----ttttttttttaccgtagggggtagcttattagttgcatcttattttataaacaagagtaagattagtgcacaaatatattcaaacctcttcaact--tgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACATCTCAGCTGTGAAGAGCCCCCAACAGGCCATTGGTGCTGCTATCAAGCA
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gatgttgtagttttatt-tcttagaaagacaatagtttaggtcccagtggattgttgtcattatgtgttatat-----cttattggaacatcttctataaatgcagGTTGGATATGCTATGCTGAAAAGACACTTGGATCCTATATTCTGCCTTATATTTCATCAGTGAAGAGCCCCCAGCAAACTATTGGAGTTACAATTAAGAAMapped 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|218489808|gb|FG954312.1|FG954312EST: CATCTGCATGCCCAG GTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACA
genomic: CATCTGCATGCCCAGgtaaaattgt ... caacttgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataaacaagagtaagattagtgcacaaatatattcaaacctcttcaacttgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACATCTCAGCTGTGAAGAGCCCCCAACAGGCCATTGGTGCTGCTATCAAGCA
cctcttc CT-rich tract
acaaatatattcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttttttaccgtagggggtagcttattagttgcatcttattttataaacaagagtaagattagtgcacaaatatattcaaacctcttcaacttgcagGTTGGATATGCTATGCAGAAAAGACTCTCGGTTCATTTATCTTGCCTTACATCTCAGCTGTGAAGAGCCCCCAACAGGCCATTGGTGCTGCTATCAAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT