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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttgtcagaactaagttttccattttaatagcatttcatactgattgatctaacattaaattatttattggccttgtgacatgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g69130.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 19
gtatgttttgtcagaactaagttttccattttaatagcatttcatactgattgatct----aacattaaattatttattggccttgtg---acatgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGC------TATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT
|||||||||  |||  ||    ||   |  || | |    ||   ||   || ||||    |||| ||  ||||    |  | ||       ||   | |||||||||||||||||||||||||| || ||  |||| ||||| ||       || ||||| ||| | ||||| |  |||||||||||||||||||||||||      
gtatgttttcgcagttctttaattcgtacattcagaagtcttggcaccacttcatctcaccaacactagcttatcacctcacgtttcttctgcaccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT------

upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 19
gtatgttttgtcagaactaagttttccattttaatagcatttcatactgattgatct----aacattaaattatttattggccttgtg---acatgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGC------TATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT
|||||||||  |||  ||    ||   |  || | |    ||   ||   || ||||    |||| ||  ||||    |  | ||       ||   | |||||||||||||||||||||||||| || ||  |||| ||||| ||       || ||||| ||| | ||||| |  |||||||||||||||||||||||||      
gtatgttttcgcagttctttaattcgtacattcagaagtcttggcaccacttcatctcaccaacactagcttatcacctcacgtttcttctgcaccatgcagACTTTGGATGAGATACCACTTGACGCAGAGGCAGTAGAGAGGGGTGGTGGATACTCCCTCGATTCTGATGCGATTGGTCTACCAAGGGCTCATGGGCTTT------
















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|38476196|gb|CF960329.1|CF960329
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|88200886|gb|CI198738.1|CI198738
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|86479683|gb|CI122316.1|CI122316
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTTC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|86478751|gb|CI121384.1|CI121384
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|25806989|gb|CA762950.1|CA762950
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|88962547|gb|CI097699.1|CI097699
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|29625093|gb|CB630104.1|CB630104
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|58683601|gb|CK072288.1|CK072288
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|29625094|gb|CB630105.1|CB630105
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
EST: gi|88840611|gb|CI080065.1|CI080065
EST:     AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAG                         ACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC
genomic: AGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCC

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: 63 (upstream exon), 65 (downstream exon)
Score: 5

AGACGACCTCTTTGCGGACATGCTCAGAGAACCCGATGAAATAACCATAAAGAGGAGGCAAATACGTGACACCCTCAAGGTCCTTCAGCAAGCATACAAGgtatgttttg ... catgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatactgattgatctaacattaaattatttattggccttgtgacatgcttcagACTTTGGATGAGATACCACTTGAAGCGGACACAGTTGAGAGAGGCTATTCCCTGGATGCCGATGCAACAGGTCTACCAAGGGCTCATGGGCTTTCTTCAT
             atctaac  putative branch site (score: 5)
       tgattgatctaacatt  TA-rich tract