Sequence
atgc intronic sequence ATGC exonic sequenceTGAGATGGTCATTGATAGTTTGGATCGGTTGATTACTGCCTGGGAGGATCGCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g39870.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G048553_T02 (Zea mays), 5'ss of exon 4
-TGAGATGGTCATTGATAGTTTGGATCGGTTGATTACTGCCTGGGAGGATCGCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcag
||| | |||||||||||||| ||||| |||||||| |||||||| | || |||||||||||||| |||| ||||||| || ||||||||||||||||| |||||||| ||| | |||| | || | || ||| ||| | | | |||||| | | || | | | || |||| ||||| | |
GATTGATTTTGATTGATAGTTTGGAACGGTTAATTACTGCATGGGAGGACAGAAAAGAATCAGTTGTTGTCGAGGTTGTTCACTTA-GCCTTAATTTTGTGgtatgtgcttccaaaaa-------actattcatttgcacatcttt-cctttcatttcagctattattattttttagat---catatcagacccactatgaagtgtagattt----------------------------------------------------------------------
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G017334_T01 (Zea mays), 5'ss of exon 4
TGAGATGGTCATTGATAGTTTGGATCGGTTGATTACTGCCTGGGAGGATCGCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaa-tagaaatagatacactatact----cactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcag
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CGAGATGGTGATTGATAGTTTGGATCGGTTAATTACTGCGTGGGAAGATAGGAAAGAATCAGTTGTTGTCGAGGGTGTTCACTTAAGCCTTAATTTTGTGgtatgtgcttccagaaa----actattcatttgcatttctttcctatcattccagctattgattcttttaggtcgtatcagacccactatattgcatttcttctgctaatagaagtggagttgttagttgtaacattcattgttaacttgcccaaattattctacatttccttttaattattccag
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv08s0040g01610.t01 (Vitis vinifera), 5'ss of exon 4
TGAGATGGTCATTGATAGTTTGGATCGGTTGATTACTGCCTGGGAGGATCGCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgcttcctaaactgttaccattatttagtttc--ccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcag
||||||||||||||| ||| | |||| |||| ||||| ||||| || || || |||||||| ||||||||||||| ||| ||||||| |||||| | || ||| || || | | |||| |||| |||| | | ||| ||||| | || | || ||| | || | || |
TGAGATGGTCATTGACAGTCTCGATCAACTGATCACTGCATGGGAAGAGCGGAAAGAATCAGTAATTGTTGAGGGTGTGCACTTAAGCCTCAATTTTATTgtgagtgtacattattct-tattctttatcggttttctgccaatctctcaagttaaatgatttaatttgttg-tcttgatggatctaa-gtaatttctttgac--------------------------------------------------------------------------------
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 5'ss of exon 5
TGAGATGGTCATTGATAGTTTGGATCGGTTGATTACTGCCTGGGAGGATCGCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcag
||||||||| ||||| ||| | |||||| |||| ||||| ||||| || || || || || || |||||||| |||||||||||||| || |||||||||||| ||| | | ||| | | | | ||| ||||| | | ||| |||| | | | ||| |||| || | | ||| |||
TGAGATGGTTATTGACAGTCTTGATCGGCTGATCACTGCATGGGAAGAGCGAAAAGAGTCGGTAGTTGTTGAAGGTGTTCACCTAAGTCTAAATTTTGTGgtaagtgtcttc---actaattctaattttttttttccttctcctgacaaggaatct-tttagtgttttgtt---tttagttaca--atggttgttccaattggcag--------------------------------------------------------------------------Mapped 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|2312028|gb|C28183.1|C28183EST: GCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTG ATGGGGCTAATGAGGGAAACATCCTTCTATAATACCTTTTATGATCTACAT
genomic: GCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgctt ... gatatttcagATGGGGCTAATGAGG-AAACATCCTTCTATAATACCTTTTATGATCTACAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAGATGGTCATTGATAGTTTGGATCGGTTGATTACTGCCTGGGAGGATCGCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA