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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA

Basic information

species Oryza sativa
transcript LOC_Os01g34614.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G146331_T01 (Zea mays), 3'ss of exon 1
gtgatggtttctctctccatcggttggattggattatggcta--gttgaattcggttcagttgtcaaattttgatatcaaatgtgattt--tctttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
    |   |||  | |  |  | ||  |     | |   |||  | |||| | ||||    ||||   | ||| ||  || | | | ||  | ||  |||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| |||||||||||||||||||| ||||||||||
---ttaccttcgatatataa-gttttcacctcctgactcctacggatgaactgggtttttctgtcgtttcttgttagaaattttaagttaatgttcttcttcagATTGCGGAGCTGAGAACACCCTGAAGCCCGGAGATGTCATCCAGTGCCGTGAATGTGGCTACCGCATCCTCTACAAGAAGCGGACCCGCCGGA

upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G41010.1 (Arabidopsis thaliana), 3'ss of exon 1
-gtgatggtttctctctccatcggttggattggatt-atggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
 |            | | ||    |        ||| ||   ||      ||   |||  ||      |||     | |  | | ||||||| | || |||||||| ||    ||||||||  ||||| | || ||||||||||| ||| | || ||||| || || || ||||||||||||||||||||  |  
agcagcctcagacatatacacttttaaaccaaaattcataagtaaaaaggttgtcttcgttttatgggttt--gcttaatttcttattttctgtatcatcagATTGTGGTCAAGAGAACACTTTGAAGTCTGGGGATGTGATCCAATGCAGAGAGTGTGGGTACCGTATTCTCTACAAGAAGCGTACCCGTAGAG

upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0079g00400.t01 (Vitis vinifera), 3'ss of exon 1
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaatt--ttgatatcaaatg--tgattttct-ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
   |  | ||   |        | ||  ||   ||||  | |  | | || | |       | ||  |  ||| |    | ||  |||   |   |||  |  ||| || ||    || ||||| |||||||| || |||||||| || |||||||||||||| || |||||| | ||||| ||||| |||||  | |
---agagctttattagtttctcgctgtttttttttat--caaaataattttgttatcaccatgaagatgtttggttcttagtggctgacccttaattggatgtagACTGTGGGCAAGAAAACACCCTGAAGCCTGGCGATGTGATTCAATGCCGTGAATGTGGTTACCGCATCTTGTACAAAAAGCGAACCCGTAGAA

upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S403_37V6.2 (Physcomitrella patens), 3'ss of exon 1
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtctt--cagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
   ||| ||||| |||  |  |   | |   || | | || | | |  |  |||    ||||    ||    ||       || || ||| | | ||  |||| || ||||| || || ||  |||| || || |||||||||||||| || || ||||| ||||||||||| ||||||||| | ||  | |   
cgcatgatttctgtctgtactgaacg-acgagagtttagc-attaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC---

upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S403_37V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtctt--cagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
   ||| ||||| |||  |  |   | |   || | | || | | |  |  |||    ||||    ||    ||       || || ||| | | ||  |||| || ||||| || || ||  |||| || || |||||||||||||| || || ||||| ||||||||||| ||||||||| | ||  | || |
cgcatgatttctgtctgtactgaacg-acgagagtttagc-attaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGCGCA

upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ25254 (Selaginella moellendorffii), 3'ss of exon 1
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
                             ||      | |  |||  | |  | |  || ||    ||||            ||| || ||  |    |||||| ||| | || ||  | || ||||| || |||||||| |||||||| ||||| |||||||||||||||||||||||| | || ||  |||
----------------------------gtgagcggcgccatgttttacttcgcttggt-gtgggttttta-----------gatctttttgtttgctagATTGTGGAACCGACAATTCGCTCAAGCCTGGGGATGTGATACAGTGCCGGGAATGCGGCTATCGCATCCTCTACAAGAAGAGAACTCGAAGGA

upper sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ23246 (Selaginella moellendorffii), 3'ss of exon 1
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgat-tttctttgtcttc-agATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA-------
                                          ||      ||      || ||     ||| | |    | | |  | | ||||| | | |||||| ||| | || ||  | || ||||| || |||||||| |||||||| ||||| |||||||||||||||||||||||| | || ||  | |       
------------------------------------------gtgagcggcgccatgcttttcttcgcttggtgtgggtttttacatctttttgtttgctagATTGTGGAACCGACAATTCGCTCAAGCCTGGGGATGTGATACAGTGCCGGGAATGCGGCTATCGCATCCTCTACAAGAAGAGAACTCGAAGAAGTAAGCG

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|88532191|gb|CI461656.1|CI461656
EST:     GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
EST: gi|58681952|gb|CK070639.1|CK070639
EST:     GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
EST: gi|88522264|gb|CI450010.1|CI450010
EST:     GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
EST: gi|29668092|gb|CB664367.1|CB664367
EST:     GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
EST: gi|88544317|gb|CI473014.1|CI473014
EST:     GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
EST: gi|29668131|gb|CB664406.1|CB664406
EST:     GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: GCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
EST: gi|58670395|gb|CK059081.1|CK059081
EST:     CGCAACTACCTGAGCCCGTGCAGCTGATCTCTGTGGAG                         ATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG
genomic: CGCAACAACCTGAGCCCGT-CAGCT-ATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTG

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: 57 (upstream exon), 74 (downstream exon)
Score: 38

TCTTGCCTCGCGCCGCCTCCGGCCGACCGCCGCGCTCCACCAGCGCCGCTGCGTCCGATGGATCCGCAACAACCTGAGCCCGTCAGCTATCTCTGTGGAGgtcattcctt ... ttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA
                     ttttgat  putative branch site (score: 38)
                                       ttttctttgtcttc  putative PPT
                  aaattttgatatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtcttcagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
-tgatggt
- - - - - - - ctccatc