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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcag

Basic information

species Oryza sativa
transcript LOC_Os05g31000.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G13850.1 (Arabidopsis thaliana), 5'ss of exon 3
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgt--gagct-tacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcag
||| ||  | ||||||||||| ||  | || || ||| |||||||||| |||||  | ||||||||||| |||||||| || ||||| ||||||||||||||  | ||| | |      |   ||||  |   | | ||| |||   |  |||   | |   || ||   |   || |   |||    ||| |||
GCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGTTAGCCGTGTCACCGTCAAAAAGAGCAAGAATgtttgtgctcttcagaaaattaaatctctcttgtgttaattgtttcctatgtt---tccaaattcattgatagaatgtggattgaaa-attgcag

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 5'ss of exon 3
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgc-----cccatttcag-------
 || ||  | |||||||| || ||  | || |||||| | ||||||||||||||  | ||||||||||| ||||| || || ||||| ||||||||||||||  |  |        |  |||  || |||||| |||  |||| ||| |   |   | |    |  |    || | |||||           ||  |       
ACAAAGCAGAAGTGAGAAGAAGAGTCGCAAAGCCATGCTCAAGCTTGGCATGAAACCCATCACTGGTGTTAGCCGAGTCACCGTCAAAAAGAGCAAGAATgtttgtgttttctctttaatattcagtcaatcttaat--ttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacag

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagctt----acgactgctcttatc----tagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcag--
|||||| ||| ||||||| ||||||||||||||||||   ||||||||||||||| |  | || | ||| | ||| |||||  ||||||||||||| |||||  || |    |   || || ||| |    || | ||||| || | || ||| |   ||| |     ||   |  | |||||    |     || |     
GCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcgtcatagcttcttttaacacgctatctaatctgaacatttatataaccgggaataagagtgtaat--gttattttccatagttaatatggcca

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagctta-cgactgctcttatctagccaatctaa-atagttctattagttggattcctgttgatgtttgctatt-tcttttgccccatttcag------
|||||| ||| ||||||| || |||||||||||||||   ||||||||||||||| |  | ||||  || |  || |||||| |||||||||||||||||||  || |  || ||     | |    |   | | |  |    || |  |      | |||  || || ||||| | ||||      |  |   |      
GCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACTGAAGTCACACGGGTTACTATCAAGAAGAGCAAGAATgtatgcctctcggcttaaagttttactcttgtttgacgtgaacctctgtgcaactgttctgcaga-gtgtgctactatcttccatatctgtctggtcaaaa

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctattt---cttttgccccatttcag------
|||||| ||| ||||||| || |||||||||||||||   ||||||||||||||  |  || | || || | |||||| ||  |||| ||||||||||| || || || |      |  |||  |       |          |  | |   ||   |   |||| ||   |  |   ||||||    | ||         
GCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAACCAGTCCCCGGCGTCACCCGTGTGACAATCAAAAAGAGCAAGAACgtaagatt-cagtgctttctattgacgtgccttgcgcttcaaaaacaatataatctttaaagatgattttaaaatagacttttggaggactttgtgcgcac

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 5'ss of exon 2
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttacgactgctcttatctagccaatctaaatagttctattagttgga--ttcctgttgatgt--ttgctatttcttttgccccatttcag-----
|||||||||| ||||||| || |||||||||||||||   ||||| || |||||| || | |||||||| |   | || ||  ||||||| |||||||||||    |   ||| |  |||    | |   |        || ||     || |  || ||  |    |  | | | ||   |       ||||  |     
GCAGAGTCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTGGGTATGAAGCCTGTGACTGGTGTCACAAGGGTGACAATCAAGAAAAGCAAGAATgtatattc-tgacagtcctttatcatctgtttatttcttttttacctcgtgaaccttgcttctcgcatcgtggatgttgtctggaatatatttttgcgtac

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|89168944|gb|CI020484.1|CI020484
EST:     AGCCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: AGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88239218|gb|CI240380.1|CI240380
EST:     AGAAGAGCAAGAAT                         ATCCTTTTCGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: AGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|218484158|gb|FG948739.1|FG948739
EST:     TGAAGTCTATCACTGGTGT-AGCCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: TGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88989765|gb|CI107452.1|CI107452
EST:     TGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: TGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88205051|gb|CI204900.1|CI204900
EST:     CCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: CCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88847917|gb|CI006103.1|CI006103
EST:     GTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: GTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88242439|gb|CI242288.1|CI242288
EST:     TGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: TGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC

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: 74 (upstream exon), 75 (downstream exon)
Score: 154

GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA