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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctttcttcccatttctttgctaaatgtgcaataacatataagatactaacagagatatcctgcccccccctgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT

Basic information

species Oryza sativa
transcript LOC_Os02g02840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 6
gtactgctttcttcccatttctttgctaaatgtgca--ataacatata-agatactaacag--agatatcctgc----ccccccctgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT
||| |||  ||| | || |  |||||||||  ||||  |||  || |  || |||||| |    ||| | ||      |||| || ||  | |||||||| |||||||| ||||||||||| |||||||| ||||||||||| || |||||||||||||||||||||| ||| ||||||||||||||||||||||
gtattgccatctgctcaatcatttgctaaacatgcacaatattatgtggaggtactaataactggatttactttttctccccacccgaatttcagAACGTGAAGGGCGTCTTCGATGCGGCGATAAAGGTTGTGCTGCAGCCGCCTAAGGCGAAGAAGAAGAAAAAGGTGCAGAGGGGGGCGTGCTCCATTTTGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 6
gtactgctttcttcccatttctttgctaa-atgtgcaataacatataagatactaacagagat-----atcctgcccccccctgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT
||| |||  ||| | ||||  |  ||||| | | |  || || |   ||  ||| || ||  |     ||  |  ||| |    || |||||||||| ||||| || ||||||||||| |||||||| ||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||
gtattgccatctgctcattcatccgctaacacgcggtatcacgtgagaggcactgacggactttacttattgtttcccacgtgaatttgcagAACGTGAAGGGTGTCTTCGATGCGGCGATAAAGGTTGTGCTGCAGCCGCCTAAGGCGAAGAAGAAGAAAAAGGCGCAGAGGGGGGCGTGCTCCATTTTGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
---------gtactgctttcttcccatttctttgctaaatgtgcaat-aacatataag--atactaacaga----gatatcctgcccccccctgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT
         ||          |  || || |     |     | |||   | | |||   | ||   ||      |||    |||   |        ||||||| || || |  ||||| ||||| ||||| |||||||| || ||||||||||||  |||||||||||||||    |||| |     |||    | | || 
ggtcacaacgtgtcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttca--ttgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAAAAACAAAAGAAC-TGTGTCATACTCTGA

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|66947308|gb|AU312152.1|AU312152
EST:     ATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: ATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|33816187|gb|CF333941.1|CF333941
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|89164703|gb|CI101791.1|CI101791
EST:     GAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: GAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|86251146|gb|CI055279.1|CI055279
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|86512832|gb|CI155465.1|CI155465
EST:     TACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: TACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|88850617|gb|CI094882.1|CI094882
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTG                         AACGTTAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|88202517|gb|CI200872.1|CI200872
EST:     ACATCGAATGCAGCTCAAAGACCCAACTA                         TACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: ACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|86489309|gb|CI131942.1|CI131942
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|33683752|gb|CF311991.1|CF311991
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|87018420|gb|CI252174.1|CI252174
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|58675807|gb|CK064494.1|CK064494
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|86260878|gb|CI066553.1|CI066553
EST:     AGCAAATAGGCGCCCCATAGTACATCGAATGCAGCTCAAAGACCCAACTT                         AACGTCAAGGGCGTTTCCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
EST: gi|7134666|gb|AU082611.1|AU082611
EST:     AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTA                         AACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC
genomic: AGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCC

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), 70 (downstream exon)
Score: 35

GGAGAGGAACTAAGAAAGCAAATAGGCGCCCCATACTACATCGAATGCAGCTCAAAGACCCAACTAgtactgcttt ... tgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaataacatataagatactaacagagatatcctgcccccccctgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT
                              tatcctgcccccccct  CT-rich tract
     ataacatataagata  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgctttcttcccatttctttgctaaatgtgcaataacatataagatactaacagagatatcctgcccccccctgatctgcagAACGTCAAGGGCGTTTTCGATGCGGCAATAAAGGTGGTGCTGCAGCCACCCAAGGCGAAGAAGAAGAAAAAGGCGCAAAGGGGGGCGTGCTCCATTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG