Sequence
atgc intronic sequence ATGC exonic sequencegttgagtagcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatcttttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g02830.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 4
gttgagtagcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatcttttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
||||||| || | || | |||| | ||||| |||| | |||| ||||||| | || ||| |||| | || | ||| | ||| | |||||||||||||| ||||| ||||||||||| || ||||||| |||||| ||||| ||||| || ||||| || || |||||||||||||| || |||||||
gttgagtgccaat------cactttcttctcccttttcagttctatcgataccatccaatgggaatgcacatatgtttgacatatttatcttcctgtttcccat-cacc--cgcagGATTATACTGCCAAACTGTCTGACTTTGGCCTCGCAAAAGATGGCCCTGAAGGTGATCAGACGCATGTGTCGACACGGGTGATGGGAACCTACGGTTATG
upper sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 4
gttgagt----agcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatctt-ttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
||||||| | || ||| | | ||| | |||||| ||| || |||| ||| |||| || || ||| |||| |||||||| || ||| | | ||||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||| ||||| |||||||||||||| |||||||||||||| || |||||||
gttgagtgttaaccacttcctcatgcttccttctcctttttcagttccattgctatcatccaatggtaatacatatatgtttgacata------tttatcttcttgtttccgttgccacagGATTATACTGCTAAGCTGTCTGACTTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATG
upper sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 4
gttgagtagcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatcttttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
|| | | | | || || | | || | || |||| ||||| || || | ||||||| | | | || | | | | |||| ||||| || ||||| ||||| ||||| || || ||||| || ||| |||| ||| ||||||||||||| || || || ||||| || ||||||||||
----gtaagtttctgatattttgaagttaattaatctgtattgtattttatgg--ctgttatgatggagttactattttttttcactgtgttcccaaatgact---------atagGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATG
upper sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 4
gttgagtagcatttcttgccaatatcttgtttttt-ttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatcttttatttgcac--ttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
| | || | ||| ||| || || | | | || ||| | ||| | ||| || || | || || || | | | | | | |||| ||||| || ||||| ||||| ||||| || || ||||| || ||| |||| ||| ||||||||||||| || || |||||||| ||||||||||||
---------cgtaagtttctggtattttgaagttaattaatctgtgttgtat---tttgtggctgttataaaatagttactaattatttttttcactgtgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT-
upper sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
gttgagtagcatttcttgccaatatcttgttttttttcctttctcttctatgcatctgttgg-gaatatgtaaatatttttcataatagcatttatcttttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
| ||||||||||||| | | || ||| | || ||| | || |||| | | | | || | | | | | | | | | |||||||||||| || || || ||||||||||| || ||||||||||| ||| |||| ||| | ||||||||||||||||| || ||||| || ||||||||||
-gtaagtagcatttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatc-------tacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATGMapped 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|58680150|gb|CK068837.1|CK068837EST: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCA GATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
genomic: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCAgttgagtagc ... acttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
EST:
gi|25799597|gb|CA755558.1|CA755558EST: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCA GATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
genomic: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCAgttgagtagc ... acttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
EST:
gi|5443728|gb|D22444.2|D22444EST: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCA GATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
genomic: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCAgttgagtagc ... acttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
EST:
gi|313081121|gb|HO213707.1|HO213707EST: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCA GATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
genomic: GGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCAgttgagtagc ... acttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAA
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:
75 (upstream exon),
72 (downstream exon)
Score:
30GATTGCATTAGGAGCTGCCAAAGGGTTAGCTTGCCTCCACAATGCTGAAAGGCCAATTATCTACAGGGATTTCAAGACATCAAATATTCTGCTGGACTCAgttgagtagc ... acttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaatatgtaaatatttttcataatagcatttatcttttatttgcacttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG
cacttac putative branch site (score: 30)
atgtaaatatttttca TA-rich tract