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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccccgcctccccgatttgacctgacatcacgcaagctcactgttaaggaattgaatctttttaagcagcattgatttgttatgagaagtttga...

Basic information

species Oryza sativa
transcript LOC_Os03g63420.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63420.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G013695_T01 (Zea mays), 5'ss of exon 1
GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccccgcctccccgatttgacctgacatcacgcaagctcactgttaaggaattgaatctttttaagcagcattgatttgttatgagaagtttga------
||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||  | ||          |   | || | |  ||||  | ||||     |      || | |    | |  |    | |   | ||  ||   |    |      
GAGGCGCTCCGGCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGCGGATGTGACATCACCGTCGgtaaactcctatatgttttg---tcacttcat-tcacagatgctcgagcctgtacgctttactgagctca--cgatctcgtggtattgggaactggcccatttgtt

upper sequence: LOC_Os03g63420.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G022248_T01 (Zea mays), 5'ss of exon 1
GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccccgcctccccgatttgacctgacatcacgcaagctcactgttaaggaattgaatctttttaagcagcatt-gatttgttatga----gaagtttga
||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||   || ||          | |    | |  ||||  | ||||   |    | | ||  ||   ||||  | |   |  |  |   ||||    | | | || 
GAGGCGCTCCGGCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGTGGATGTGACATCACCGTTGgtaa--actcctttatatttttctcgtttcat-tcacagatgctcgaggc-gggaatttctatacgtttatactgagctcaagatcccatgatattggaatctg-

upper sequence: LOC_Os03g63420.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ21411 (Selaginella moellendorffii), 5'ss of exon 1
GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcacc-ccgcctccccgatttgacctgacatcacgcaagctcactgttaaggaattgaatctttttaagcagcattgatttgttatgagaagtttga
|| |  ||||||||||| |||||||  ||||||| ||||||||| || || |||||||||||||| ||||||||||| || || ||||| |||||  | |||| |     |   |||| |    |     ||     | ||||    ||  |      ||   |||||||   |||                         
GATGGCCTCCGCCAGGGCCTCAAGGCCTACTCCAACTGGCCCACTTTTCCACAGCTCTACATCGATGGCGAGTTCTTTGGTGGCTGCGATATCACTCTCGgtaagtttagctatctcctctccatcgatcgatcaagctcaagaattctcctcg---cttttctcttttttgccag-------------------------

upper sequence: LOC_Os03g63420.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ23774 (Selaginella moellendorffii), 5'ss of exon 1
GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcacc-ccgcctccccgatttgacctgacatcacgcaagctcactgttaaggaattgaatctttttaagcagcattgatttgttatgagaagtttga
|| |  ||||| ||||| |||||||  ||||||| ||||||||| || || |||||||||||||| ||||||||||| || || ||||| |||||  | |||| |     |   |||| |    |     ||     |  |||    ||  |      ||   |||||||   |||                         
GATGGCCTCCGTCAGGGCCTCAAGGCCTACTCCAACTGGCCCACTTTTCCACAGCTCTACATCGATGGCGAGTTCTTTGGTGGCTGCGATATCACTCTCGgtaagtttagctatctcctctccatcgatcgatcaagcttaagaattctcctcg---cttttctcttttttgccag-------------------------

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|88557522|gb|CI487937.1|CI487937
EST:     NCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAGAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88661678|gb|CI458188.1|CI458188
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88992227|gb|CI035365.1|CI035365
EST:     CATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCGATGTTAT
genomic: CATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88974591|gb|CI022132.1|CI022132
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|86508177|gb|CI150810.1|CI150810
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|87025835|gb|CI282412.1|CI282412
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGAGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88295904|gb|CI535067.1|CI535067
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88211020|gb|CI212453.1|CI212453
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88981247|gb|CI026955.1|CI026955
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88530437|gb|CI458832.1|CI458832
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88478158|gb|CI415429.1|CI415429
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88513905|gb|CI441411.1|CI441411
EST:     GCAGCTGTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88461454|gb|CI526962.1|CI526962
EST:     GCAGCTCTACATCGAGGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGGTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88661689|gb|CI458325.1|CI458325
EST:     NCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|86531224|gb|CI171430.1|CI171430
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
EST: gi|88321490|gb|CI535442.1|CI535442
EST:     GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTG                         ATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT
genomic: GCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTAT

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: 67 (upstream exon), 74 (downstream exon)
Score: 73

GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccc ... tattttgcagATGCATACAAAAGTGGAGAGCTGCAGGAAACACTAGAGAAAGCAATGTTATCTTAGTATAAACGTCGAAACACACCATAGAGTACATATAAATGGTATAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCGCTCCGCCAGGGGCTCAAGGAGTACTCCAGCTGGCCCACCTTCCCGCAGCTCTACATCGACGGCGAGTTCTTCGGAGGATGCGACATCACCGTTGgtacgcaccccgcctccccgatttgacctgacatcacgcaagctcactgttaaggaattgaatctttttaagcagcattgatttgttatgagaagtttga

- - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc