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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaattccacattcttgtcaatgtttcaaaaaattaagttgacttcttgtgccaatttcttaacattagcgtgatgctttatttacag

Basic information

species Oryza sativa
transcript LOC_Os01g53700.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G43000.1 (Glycine max), 5'ss of exon 8
ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaattccacattcttgtcaatgtttcaaaaaattaagttgacttcttgtgccaatttc----tta-acattagcgtg-atgctttatttacag-
||||| |||||||||||||| || ||||||||||| || ||||| || || ||||||||  |  |||||| |||  |  | | ||  |  || |  || ||    |||  |   | |  |||    |  ||     ||| | ||| |  |  ||    | ||  ||  
ATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGTgtaagttttac-ctatatcttcttctactttacagctgattttggccaatgtttgatttacctttgccattatatatttgtatttataaacttttcccatt

upper sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 7
ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttg---aattccacattcttg---tcaatgtttcaaaaaattaagttgactt-cttgtgccaatttcttaacattagcgtgat--gctttatttacag
||||| |||||||||||||| ||||||||||||||||||||||| || || ||| | || ||| | |||| |||    |  | ||||    ||   |||  |||| ||    | | |||||  | | ||   ||  || |  | | | | |   |  |  ||   ||   
ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTATgtaagtttctcagatacacacgtgtgcattcagagttttaag--ttgaggttgagatacatgcaacacattttgcatacttgtgcattcagtattgcatatg-

upper sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S74_253V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaattccacattcttgtcaatgtttcaaaaaattaagttgacttcttgtgccaatttcttaacattag---cgtgatgctttatttacag-------------
                           |||  | |||||||| || ||||||||||| ||||||||||| ||||| ||| ||||||||||||  |  | |  |   | ||| |    | | | | |       ||  |   |  ||  |  | |||||   ||||     |||     | | ||||                
TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACAC-TGGGgtaagatattatccggagtatcttatcgtga-aaactctttctttaagatagtttctggtcattgatttcgtagaagtctgtttatgtttcgggtaatcaa

upper sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S219_95V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgt---tgaattccacattcttgtcaatgtttcaaaaaattaagttgacttcttgtg-ccaatttcttaacatta----gcgtgat-gctttatttacag----------------------------------------------------------------------------
                            ||  | |||||||| |  ||||||||||||||||||||||| ||||| |||   |||||| |||  | |    | |  |||||    |||| ||    |   |  ||||  |||    ||  |     ||        || |    || ||||  |   || ||||                                                                             
TTCGTGTGCTGTGACGGTTTTGCAATCTCTTCTAGGAGGAGGAGCGTCTTTCTCTGCTGGTGGTCCTGGAAAGGGAATGTTCTCTCGACTGTACACGCGGgtaagatccaccacattgtgaagtccttgtaccattatattggaagctaataattgatgagagggtataatagggcatgattacggcatctacataagccttcattttatgaacttgactggtttgaatgtttgccgaaggaacctcatgtgggcactttcgtcatttcag

upper sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S37_50V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtat---gttgaattc--cacattcttgtca-atgtt--tcaaaaaattaagttgacttcttgtgccaatttcttaacattagcgtgatgctttatttacag-----------------------------------------------------------------------------
                         |  ||| | |||||||| || ||||| ||||||||||||||||| ||||| ||| | |||||||||| ||    | | |   |  | ||||     || | | |  |  |   |||| || |    ||  |  | |||| |  |     | |   |   | ||    |                                                                              
TTCCTATGCTGTGACTGTCTTGCAAACACTCCTTGGAGGAGGGGGGTCTTTTTCTGCTGGTGGTCCTGGAAAGGGAATGTACTCTCGATTGTATACAGGGgtaagaccggcgcattggcaacagaagctggttcattgattatgtagcaggctgttcacgatttgtagaggcaggagcattttctgatgagtaaacttgccaatgagatttttgacctgaacatcgtatttgatttcttactttattttgatttatctgttttatttgcag

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|27554475|gb|CA998375.1|CA998375
EST:     GCTCTTTCTCTGCTGGCGGCTCCTGGGAAGGGCCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACAACTACCATCACATCGAGCCATTCTCTGCATTCA
genomic: GTTCTTTCTCTGCTGGTGG-TCCTGGGAAGGGC-ATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
EST: gi|27577068|gb|CA999762.1|CA999762
EST:     TGG-TCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
genomic: TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
EST: gi|38475250|gb|CF959383.1|CF959383
EST:     TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
genomic: TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
EST: gi|9864980|gb|AU100730.1|AU100730
EST:     ATGCATTTCTCGATTGT                         ATCCCCCGGATATTAAAACAACTACCCATCAGATCGAGTCATTCTCTGCAT
genomic: ATGCA-TTCTCGATTGTgtatgttgaa ... ttatttacagAT-CTCCGGATATT-AAACAACTA-CCATCAGATCGAGTCATTCTCTGCAT
EST: gi|58690219|gb|CK078906.1|CK078906
EST:     TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
genomic: TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
EST: gi|300215819|gb|HO088445.1|HO088445
EST:     TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
genomic: TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
EST: gi|2311057|gb|C27212.1|C27212
EST:     TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACANCTACCATCAGATCGAGTCATTCTCTGCATTCA
genomic: TGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
EST: gi|163920798|gb|EG710061.1|EG710061
EST:     AAGGGCATGCATTCTCGATTGT                         ATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA
genomic: AAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCA

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), 70 (downstream exon)
Score: 31

ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaa ... ttatttacagATCTCCGGATATTAAACAACTACCATCAGATCGAGTCATTCTCTGCATTCAACAGTATCTACAACCATTCTGGTCTTTTTGGAATTCATGCAACAACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGTgtatgttgaattccacattcttgtcaatgtttcaaaaaattaagttgacttcttgtgccaatttcttaacattagcgtgatgctttatttacag

- - - - - - - - - - - - - - - - TGGTGG