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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattgtcagtggcttgcttaaacaacatcaacagttcttttaaaagatgggtttgatagggaaacacatgaatactgacacccaacttctgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA

Basic information

species Oryza sativa
transcript LOC_Os03g03410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 3
----atattgtcagtggcttgctta-aacaacatcaacagttcttttaaaagatgggtttgatagggaaacacatgaatac-tgacacccaacttctgc-tctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA
    | ||  |||     ||  ||        |  |||| |       |||||||    |||||| |||| |   ||| || |||||  |||||||| | |  | ||| |||| |||||||| ||||||||||||||||||||||| || |||||||||||| ||||||| || |||||||||||||| ||||| |||| ||| || 
gcttaaatgatcaagcctttatttttggttgaaaaaacaat-------aaagatgcagatgatagtgaaatatccgaaaacctgacattcaacttctacatacccagGTTGGCTTATCTTCACGAGGGGCTGGAACCGAAGGTTGTTCACCGTGACATCAAAGCTAGCAACATTCTTCTTGACCAGCAGTGGAACGCTAGAGTATCC

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G317938_T01 (Zea mays), 3'ss of exon 3
atattgtcagtggctt--gcttaaacaacatcaaca-gttcttttaaaagatgggtttgatagggaaacacatgaatactgacacccaacttctg-----ctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA
        | ||||||  ||  |||| |   || |      |||| |  ||||     ||||| ||||||   ||| ||||||| ||||||| ||     | | | ||||||||||| || || |||||||||||||||||||| ||||| || ||||||||  ||||||| ||||||||||||||||| ||||| || ||||| || 
--------attggcttttgcagaaacgatcacagcctagctttttgattgatgcaaacgatagtgaaacatccgaaaactgacatccaacttgtgtacatccccccagGCTGGCCTACCTCCACGAGGGGCTGGAACCGAAGGTGGTCCACCGCGACATCAAGGCTAGCAACATCCTTCTTGACCAGCAGTGGAACGCCAAAGTATCG

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 3
atattgtcagtggcttgcttaaacaacatcaacagttcttttaaaagatgggtttgatagggaaacacatgaatactgacacccaacttctgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA
 ||  ||   ||   || |||| |  |||  |      | |   | ||||   ||||| |         |||  ||||         ||   || |  ||  ||||||||||||||||||| || |||||||| |||||||| || ||  | ||||| || || || ||| |||| |  ||||||||  | || || || 
gtaccgtatttg---tgattaatcttcatacattaaaatctctgatgatg--cttgattgt------tttgataactgtgctttttgtttatcttttcagATTGGCCTATCTTCATGAGGGTCTTGAACCGAAAGTTGTCCACCGAGATGTGAAATCAAGTAACATACTTATTGATCGCCAATGGAACTCCAAGGTTTCC

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G01330.1 (Arabidopsis thaliana), 3'ss of exon 3
atattgtcagtggcttgcttaaacaacatcaacagttcttttaaaagatgggtttgatagggaaacacatgaatactgacacccaacttctgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA
         ||    | |  | |  ||  |     |   ||| |    ||  ||  ||        | |||     ||       |  |     |   ||  |||||||||| |||||||| || |||||||| || || ||||| ||||| |||||||| |||||  | ||||| |  |||||||||||||| || |||
---------gtacacttccgaga-gacgcctttgataactttcatttgtgaattc-atctttttctatatgtgatttgtttgttgatatt---cccgcagATTGGCCTATCTGCATGAGGGTCTTGAACCGAAAGTCGTTCATCGGGACATAAAATCTAGTAATATTTTGCTTGATCGTCAATGGAATGCTAAGGTATCA

upper sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 3
atattgtcagtggcttgcttaaacaacatcaacagttcttttaaaagatgggtttgatagggaaacacatgaatactgacacccaacttctgct-ctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA
 ||    |  | |  || |  |   | | | |     |||||    ||     ||| | || |      |  |   ||     | | || || | || |||  ||||||||||||||||||| || ||||| |||||||||||||| ||  | ||||||||||| || || ||||| |  ||||||||  |||| ||||| 
gtacctaccctagtctgatatactgaaaactatccaacttttgcccgaaaacattgcttggcaggttgttctaatgtgctttgctatttttgttgctgtagATTGGCCTATCTTCATGAGGGTCTTGAACCAAAGGTTGTCCATCGAGATGTAAAATCTAGCAACATACTACTTGATCGCCAATGGAACTCTAAGGTGTCT

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|125863442|gb|EL586716.1|EL586716
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|58680434|gb|CK069121.1|CK069121
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGTGGGCTAGAACCGAAGGTTGTCCATCGTGACA
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAG-GGGCTGGAACCGAAGGTTGTCCATCGTGACA
EST: gi|38480926|gb|CF965015.1|CF965015
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|58687074|gb|CK075761.1|CK075761
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|38477229|gb|CF961362.1|CF961362
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAGTTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|58680836|gb|CK069523.1|CK069523
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAG
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAG
EST: gi|58588930|gb|CF987238.1|CF987238
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|58694780|gb|CK083467.1|CK083467
EST:     CCACTAACTTGGGAAGTCAGGATGAGCATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|300215530|gb|HO088156.1|HO088156
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT
EST: gi|58693941|gb|CK082628.1|CK082628
EST:     CTAACTTGTGGAAGTCAGTGATGAACATAATTCTTGGAACTGCTAAAGTG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACA
genomic: CTAACTTG-GGAAGTCAG-GATGAACATAATTCTTGGAACTGCTAAAG-Ggtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACA
EST: gi|58688663|gb|CK077350.1|CK077350
EST:     CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGG                         GCTGGCCTATCTTCATGAGGGGCTAGAACCGAAGGTTGTCCATCGTGACAT
genomic: CCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACAT

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: 72 (upstream exon), 74 (downstream exon)
Score: 27

ACAACGGCAATCTTGATCAATGGCTTCATGGTGATGTAGGGGAAGTGAGCCCACTAACTTGGGAAGTCAGGATGAACATAATTCTTGGAACTGCTAAAGGgtaatgcttc ... tgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgggtttgatagggaaacacatgaatactgacacccaacttctgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA
                            tactgac  putative branch site (score: 27)
                                         cttctgctctct  putative PPT
       tttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattgtcagtggcttgcttaaacaacatcaacagttcttttaaaagatgggtttgatagggaaacacatgaatactgacacccaacttctgctctctagGCTGGCCTATCTTCATGAGGGGCTGGAACCGAAGGTTGTCCATCGTGACATCAAATCTAGCAATATCCTTCTTGACCAGCAATGGAATGCTAAAGTGTCA

- - - - - -ggcttgc
- - - - - - - - - - -aacaaca
- - - - - - - - - - - - - - - - - - - - - aaaagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacac