Sequence
atgc intronic sequence ATGC exonic sequencegtaaagcataggttttgtgtataagatctgttttattaactgtaggcttttaagactctcctgttgagattataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g28010.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G029038_T01 (Zea mays), 3'ss of exon 2
gtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgaga-----ttataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
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gtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaatttcgtatcttcaaatcgtccactggaaaacaaactaaaacagATGATTATGGTAAGAGAAGAAAATGATCCTGCTCCAGAAGGAGTTGAGTACAAGCATGGGCTTACTCCTCTAATGAGGGATGCACGCAGGCGACGTTTCC
upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G454830_T01 (Zea mays), 3'ss of exon 3
gtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgaga-----ttataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
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gtaaaagtgcatgtttaatgtatgtcacctatttatttattaaatttcgtatcttcaaatcgtccactgaaaaacaaactaaaacagATGATTATGGTAAGAGAAGAAAATGATCCTGCTCCAGAAGGAGTTGAGTACAAGCATGGGCTTACTCCTCCAATGAGGGATGCACGCAGGCGACGTTTCC
upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147614_T01 (Zea mays), 3'ss of exon 3
gtaaa-gcataggttttgtgtataagatctgttt---tattaactgtaggcttttaagactctcctgttgagat----tataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
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gtaaaagtgcatgtttaatgtatgtcacctgtttatttattaaacttcgtatcttcaaatcgtccactgaaaacaaactgaaacagATGATTATGGTAAGAGAAGAAAATGATCCTGCTCCAGAAGGAGTCGAGTACAAGCATGGGCTTACTCCTCCAATGAGGGATGCACGCAGGCGACGTTTCC
upper sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagcataggtt--ttgtgtataagatctgttttattaactgtaggcttttaagactctcctgttgaga----ttataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
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gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTCMapped 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|88732456|gb|CI755633.1|CI755633EST: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAG ATGATCATGGTAAGAGAAGA
genomic: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGA
EST:
gi|88223765|gb|CI223614.1|CI223614EST: GCTGATATTGGTCAG ATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
genomic: GCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
EST:
gi|88977292|gb|CI025029.1|CI025029EST: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAG ATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
genomic: ACAAGACATATGATGATTCAGTGCTAATTAAAACAGCTGATATTGGTCAGgtaaagcata ... attataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatctgttttattaactgtaggcttttaagactctcctgttgagattataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
tattaac putative branch site (score: 1)
ttttattaactgta 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagcataggttttgtgtataagatctgttttattaactgtaggcttttaagactctcctgttgagattataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC