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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgctcctcttgatcccgtggcggtggcgggctgcctgatcttgatccgcggcgagcggtggtggtggtggtggtggtgtggtttctcgttggg...

Basic information

species Oryza sativa
transcript LOC_Os01g12880.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G062953_T01 (Zea mays), 5'ss of exon 1
TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgctcctcttgatcccgtggcggtggcgggctgcctgatcttgat-ccgcggcgagcggtggtggtggtggtggtggtgtggtttctcgttggg----
|||| || |||||||||||||| || ||||| |||||||||||||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||   |  || ||   |||||   |  || |  |   |    ||  | | |  | || | | |      |     |    | | | ||     | | |    
TGGCTGGTTCCATGGTGGACCGCGCCACCAGAGACATGCTCATCGGCCCGGACTGGGCTAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacg---gaccccctc--tcccgctaccctgacctgtctcggattcgggctgctcccgccatcagattccctccctatccccgcgagattctcaatcgcgcctg

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G153138_T02 (Zea mays), 5'ss of exon 1
TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgctcctcttgatcccgtggcggtggcgggctgcctgatcttgatccgcggcgagcggtggtggtggtggtggtggtgtg-gtttctcgttggg-
|||| ||||||||||||||||| || |||||||||||||||||| | || |||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||   | ||   |   ||||    | |      | |  |     || |||||  |  |      |       | |    |    | ||   |  |   
TGGCAGGCTCCATGGTGGACCGCGCCACCAGCGACATGCTCATCAGCCCGGACTGGGCTAAGAACATGGAGATCTGCGACATATGCAACCGCGACCCTGGgtacgta--cccccactccccccgctctgatccttctcagattcgggctgctccgccaccgggttccctccctcccgcgagattccatgcttactgccgata

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G26440.1 (Glycine max), 5'ss of exon 1
TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgctcctcttgatcccgtggcggtgg--cgggctgcctgatcttgatccgcggcgagcggtggtggtggtggtggtggtgtggtttctcgttggg
||| |   ||||||||||| || || || |||||||||||||| ||||| || ||||||| |||||| ||||||||||||||   ||| |  ||||| |||| ||| | |   | |||  | | |  |       ||  | |  |     | ||||||     |||       |  |  || |  | |    | |  | |  
TGGTGAATTCCATGGTGGAACGCGCCACGAGCGACATGCTCATAGGGCCTGATTGGGCCATGAACATCGAGATCTGCGACATGCTCAATCATGACCCTGGgtgcgttttccttttttgcactctttcctccaaaacgcaccgtttttctctaatccgccaaacgcgaatcatctttttttgtttttttatcgttttttcg--

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA14G21410.1 (Glycine max), 5'ss of exon 1
TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc-tcctcttgatcccgtggcggtggcgggctgcctgatcttgatccgcggcgagcgg-tggtggtggtggtggtggtgtggtttctcgttggg
||| |   ||||||||||| || || || |||||||||||||| |||||||| ||||||| |||||| ||||||||||||||   ||| | |||||| |||| ||| | | | |||    ||      | |   ||  | |  |  |  | ||||||     |||  |  |  |  | ||     | || |   |  |||  
TGGTGAATTCCATGGTGGAACGCGCTACGAGCGACATGCTCATAGGGCCCGATTGGGCCATGAACATCGAGATCTGCGACATGCTCAATCACGACCCTGGgtgcgttttccttctcgcactctttcctccgaaacgcaccgtttt-ttctaatccgccaaacgcgaataatcttttttgtttgtttttgatcattttttgc-

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ20837 (Selaginella moellendorffii), 5'ss of exon 1
TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgctcctcttgatcccgtggcggtggcgggctgcctgatcttgatccgcggcgagcggtggtggtggtggtggtggtgtggtttctcgttggg
                 ||   |||||| |||||||||||||| || ||||| ||||||| |||||||||||| || || |||  ||||| ||| || ||||| || ||||||    ||        |     || |||  |     |  ||  |     | |  |                                  
-----------------GATAAGGCGACGAGCGACATGCTCATAGGACCCGATTGGGCCATGAACATGGAGATATGTGATATCCTCAACCACGATCCTGGgtaagtttgctccag--gaagtaaaaaccagctcgagctcacacgattcaattggaaaaaaactttttccag----------------------------

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|88694259|gb|CI738297.1|CI738297
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88398026|gb|CI585529.1|CI585529
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88718071|gb|CI741581.1|CI741581
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88404185|gb|CI575673.1|CI575673
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88744503|gb|CI767863.1|CI767863
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|29674265|gb|CB670540.1|CB670540
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|86903843|gb|CI302489.1|CI302489
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88299682|gb|CI577184.1|CI577184
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88411131|gb|CI606350.1|CI606350
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88363396|gb|CI617957.1|CI617957
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88377286|gb|CI600441.1|CI600441
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|24208345|gb|AU225372.1|AU225372
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88761808|gb|CI771364.1|CI771364
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88390599|gb|CI609224.1|CI609224
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
EST: gi|88371552|gb|CI602730.1|CI602730
EST:     GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGG                         GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA
genomic: GACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAA

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: 70 (upstream exon), 74 (downstream exon)
Score: 46

TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgc ... tcatgtacagGCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGGGCTCCATGGTGGACCGGGCGACCAGCGACATGCTCATCGGGCCCGACTGGGCCAAGAACATGGAGATCTGCGACATCTGCAACCGCGACCCCGGgtacgtgtgctcctcttgatcccgtggcggtggcgggctgcctgatcttgatccgcggcgagcggtggtggtggtggtggtggtgtggtttctcgttggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtgg