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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatcatgcacaacattttgttatgcagcaatgaacgaatcttcaagttggttggtcgagtttttttatataaaaatgttctggatgttacag

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G143651_T01 (Zea mays), 5'ss of exon 9
TGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatcatgcacaacattttgttatgcagcaatgaacgaatcttcaagttggttggtcgagtttttttatataaaaatgttctgg-atgttacag
|||||||||||||||||| |||||||| |||||||||||||| |||||||||||||  || |||||||| || || || ||||| ||||| ||||||||||||| | | |  | |||| | | |  ||| |   |||    ||| | ||  |  |  ||   |        || | |  ||| |  ||  | | ||||
TGTTGCTGCTGCTATTGTGAACTCCCTGAAGGATGACGGCACTAGCATGGGAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgttactc-caacttgtggcgatgaat--atgttttaatttgcatatgtgaagggaaaaagag---atgtgaccatgattgggtgtatgacag
















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|11442907|gb|BF430806.1|BF430806
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|4714677|gb|AU055794.1|AU055794
EST:     AGAGTTTTATACCTGTTCATGGAGCTG                         GCTGAGCTGATGTATGAGCCAATTACGTGAATGGCCACGGTACATCGATG
genomic: AGAGATTTATA-CTGTTCAT-GAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAA-TACGTGAATGGCCACGGTACATCGATG
EST: gi|86422921|gb|CI060494.1|CI060494
EST:     AGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACGATACGTGAATGGCCACGGTACATCGATGTT
genomic: AGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|88246401|gb|CI246250.1|CI246250
EST:     CTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: CTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|29673109|gb|CB669384.1|CB669384
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|88227607|gb|CI227087.1|CI227087
EST:     GACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|86423690|gb|CI062451.1|CI062451
EST:     GAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|86831290|gb|CI297559.1|CI297559
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|86599963|gb|CI258303.1|CI258303
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|86435376|gb|CI106609.1|CI106609
EST:     ACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCCCGGTACATCGATGTT
genomic: ACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|29671359|gb|CB667634.1|CB667634
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|8856604|gb|AU093922.1|AU093922
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
EST: gi|88730417|gb|CI754030.1|CI754030
EST:     GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTG                         GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT
genomic: GAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTT

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: 75 (upstream exon), 67 (downstream exon)
Score: 58

TGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatca ... gatgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCAGAGATTTATACTGTTCATGAGCTGgtaattatcatgcacaacattttgttatgcagcaatgaacgaatcttcaagttggttggtcgagtttttttatataaaaatgttctggatgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA