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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgttaccatgattttgttaagtcggttagcatgctgtatacttattgcatgtttttgtgcgacccaactaaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG

Basic information

species Oryza sativa
transcript LOC_Os07g12110.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 2
---gttgttaccatgatt---ttgttaagtcggttagcatgctgtatacttattgcat-gtttttgtgcgacccaac-taaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG
   ||  ||   ||||||   ||||| | |    |   ||| | |  |  | | |  | |||| |||       |||  ||||  |  |   | || |       ||||||||||| || ||||||||| || |||| ||||  ||||||||||||||||| || || || || || | ||||||||  ||  | || || ||| |  
gttgtgatttggatgattaagttgtttaattttgtgaaatgttatccagatttggttttgtttgtgtattgtggaacacaaatcttatatggcttggtgtcttatcagATTGGTCCAGACCAGATTGAGGCTTTGTACCAGTACGCCAAGTTTCAGTTTGAATGTGGCAACTATTCTGGTGCTGCTGATTATCTTTACCAGTACAGGA

upper sequence: LOC_Os07g12110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S363_21V6.2 (Physcomitrella patens), 3'ss of exon 2
gttgttaccatgattttgtta-agtcggttagcatgctgtatacttattgcatgtttttgtgcga-cccaactaaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG
 |||| |     |   | |   | |       | ||||   | | | | | |||      |   |  |  ||    |  || || |  || |  |  || |||| ||| ||||||| || ||| |||||||||||| ||||||||| |||||||| ||||| || ||||| | |||  | | |||| ||||| | || || |
attgtaatatgtagcatatcgcatttcaacgtcttgctacctccgtgt-ggatgccacattataagtctgacagtttcgtctaaattgtgattgtt-tgtagATCGGTTCTGAGCAAATCGAGGCTCTGTATCAGTATGCCAAGTTCCAGTTTGAGTGCGGAAACTACTCGGGTGCATCCGACTACCTGTATGAGTATCGCG
















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|38471465|gb|CF955596.1|CF955596
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|29688863|gb|CB685138.1|CB685138
EST:     GCCAGACAAGCAG-CCTAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
genomic: GCCAGACAAGCAGTAC-AACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58657959|gb|CK046639.1|CK046639
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|29630664|gb|CB635673.1|CB635673
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58693227|gb|CK081914.1|CK081914
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|33794825|gb|CF323292.1|CF323292
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58600665|gb|CK011193.1|CK011193
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|29617589|gb|CB622601.1|CB622601
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|33794207|gb|CF322994.1|CF322994
EST:     CAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: CAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58669221|gb|CK057907.1|CK057907
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58687118|gb|CK075805.1|CK075805
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58694037|gb|CK082724.1|CK082724
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|218501745|gb|FG957162.1|FG957162
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58654411|gb|CK043091.1|CK043091
EST:     TCAGGCCAGACAAGCAGTACAAGCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|88367667|gb|CI568439.1|CI568439
EST:     TCAGGCCAGACAAGCAGTA-AACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTAT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTAT
EST: gi|33795947|gb|CF323841.1|CF323841
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|33793903|gb|CF322840.1|CF322840
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58694550|gb|CK083237.1|CK083237
EST:     GCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: GCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|29682305|gb|CB678580.1|CB678580
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|29628320|gb|CB633331.1|CB633331
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58657385|gb|CK046065.1|CK046065
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|29645460|gb|CB650467.1|CB650467
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|33653756|gb|CF276370.1|CF276370
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGGGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58694994|gb|CK083681.1|CK083681
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|58666438|gb|CK055124.1|CK055124
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTACTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT
EST: gi|117243527|gb|CT843109.1|CT843109
EST:     TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAG                         ATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTATGCCAAGTTTCAGTTT
genomic: TCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTT

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), 74 (downstream exon)
Score: 60

CACCGCCCCCATCGTCTCCTTCCTCCAGAACCAGCAGCTCGTCCAGGAGCTCAGGCCAGACAAGCAGTACAACCTCCACATGCTCCAGGACCGCTTCCAGgtcgatctac ... aatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcatgtttttgtgcgacccaactaaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG
                      aactaaataatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttaccatgattttgttaagtcggttagcatgctgtatacttattgcatgtttttgtgcgacccaactaaataatcaaactcctgttaatgatgcagATTGGTCCTGAGCAGATTGAGACTCTGTATCAGTTTGCCAAGTTTCAGTTTGACTGCGGTAATTACTCAGATGCTGCTGTCTACTTGTATCAATACCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -taccatg
- - - - - - - - - - - - - - -agcatgc
- - - - - - - - - - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa