Sequence
atgc intronic sequence ATGC exonic sequence...tcatctttgtgatcgatacatctctttatgcaacttttgttctcattaaactgtcacctcaaaaatttatgaatgaatatgtaaatcaaacaccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTGTCCACTTTGCCGGAGAAGAATTGACCAAGCTGTGAGAACTTTCCGCCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g45350.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G020574_T05 (Zea mays), 3'ss of exon 10
-tcatctttgtgatcgatacatctctttatgcaacttttgttctcattaaactgtcacctcaaaa-atttatgaatgaatatgtaaatcaaac---accgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTGTCCACTTTGCCGGAGAAGAATTGACCAAGCTGTGAGAACTTTCCGCCAT
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tgcagatatgcga---atttgttcataattatagcctttgctatcattg--ttgtcaccgctgaatgtttctgtttggactttaaagtgacttctaattacacagGTGTGGTCACATGTGTTGCTGTGTGGCATGCTCTTCACATTTGACGAACTGCCCACTTTGCCGGAGAAGAATTGACCAAGCTGTCAGAACCTTCCGCCAT
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 10
------tcatctttgtgatcgatacatctctttatgcaacttttgttctcattaaactgtcacctcaaaaatttatgaatgaatatgtaaatcaaacaccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTGTCCACTTTGCCGGAGAAGAATTGACCAAGCTGTGAGAACTTTCCGCCAT
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gatatgtgaaattcgttcataatttgtc-cttgctatcactgttgtcacccctgaaagtttctgtttggactttaaaagtga-----ttaatccaatgttacacagGTGCGGTCACATGTGTTGCTGTATGGCATGCTCTTCACATTTGACAAACTGCCCGCTTTGCCGGAGAAGAATTGACCAAGCTGTCAGAACATTCCGCCAT
upper sequence: LOC_Os07g45350.4 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 10
tcatctttgtgatcgatacatctctttatgcaacttttgttctcattaa------actgtcacctcaaaaatttatgaatgaatatgtaaatcaaacaccgtg-----cagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTGTCCACTTTGCCGGAGAAGAATTGACCAAGCTGTGAGAACTTTCCGCCAT
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----------aaacaatacttttcttttaaccatttctagttctatttattgtttgttgacctgttcagaattta-aaatgagcaaatggtttactgtccatggttctcagGTGTGGCCATATGTGCTGTTGTACAATGTGCTCTTCTCAGTTGACCAACTGTCCACTTTGCCGACGACGGATCGAGCAGGTAGTAAGGACTTTCCGTCACMapped 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|33683627|gb|CF311866.1|CF311866EST: GACATATGTGTCATATGCCTTGAACAGGAAT-TNATGCTGTTTTTGTGCC GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
EST:
gi|86905521|gb|CI285484.1|CI285484EST: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCC GTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
genomic: GACATATGTGTCATATGCCTTGAACAGGAATATAATGCTGTTTTTGTGCCgtaagtatct ... caccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaactgtcacctcaaaaatttatgaatgaatatgtaaatcaaacaccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTGTCCACTTTGCCGGAGAAGAATTGACCAAGCTGTGAGAACTTTCCGCCAT
aaaaatttatgaatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatctttgtgatcgatacatctctttatgcaacttttgttctcattaaactgtcacctcaaaaatttatgaatgaatatgtaaatcaaacaccgtgcagGTGTGGCCACATGTGCTGCTGTATGAACTGCTCTTCTCATTTGACGAATTGTCCACTTTGCCGGAGAAGAATTGACCAAGCTGTGAGAACTTTCCGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG