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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctattagaaatctgtaatggacacgaatagatgatctcttgcatgcttgcaaaccccagtacctgtataaacttcttatgctctgcacttattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGCGATCTCTCATGTCGCCGGCAAGATACCTGTTTCCTCGTCAGATTTGGAA

Basic information

species Oryza sativa
transcript LOC_Os04g32150.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G155962_T03 (Zea mays), 3'ss of exon 9
-cctattagaaatctgtaatggacacgaatagatgatctcttgcatgcttgcaa-accccagtacctgtataaacttcttatgctctgcacttattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGCGATCTCTCATGTCGCCGGCAAGATACCTGTTTCCTCGTCAGATTTGGAA
   |||    ||| | |||   | |  |     | ||    ||  | |  |||  | |    || |   ||  | |  |||||||||| || | || ||||||||||||||||  ||||||||||||||||| |||||||| |  | ||||||||| |||||||||||| |||||||||| ||||||  |||||||||||||
tattatattgaatatataaataatataatccctttattctctg-gtacgagcactatcggtctatcgccatggattaattatgctctggacatgtt-tgcagTGACTTCCCCTATGTTGTTCCTGAATGTGGTTACAAAGGAGGAAGGGAGGCGATTTCTCATGTCGCCAGCAAGATACCAGTTTCCCAGTCAGATTTGGAA
















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|88838528|gb|CI375076.1|CI375076
EST:     CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88561802|gb|CI492519.1|CI492519
EST:     CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88661256|gb|CI450506.1|CI450506
EST:     GGAGCGAATCGAATAATGTGGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGG
genomic: GGAGCGAATCGAATAATGT-GGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGG
EST: gi|88461866|gb|CI506942.1|CI506942
EST:     AGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: AGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88518536|gb|CI446190.1|CI446190
EST:     ATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: ATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88491138|gb|CI428410.1|CI428410
EST:     CTCTAGCTATGGAGCGAATCGAATAATGTGGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGG
genomic: CTCTAGCTATGGAGCGAATCGAATAATGT-GGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGG
EST: gi|88480299|gb|CI417570.1|CI417570
EST:     GCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: GCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88520438|gb|CI448092.1|CI448092
EST:     TGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: TGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88419086|gb|CI511238.1|CI511238
EST:     ATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: ATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|87034372|gb|CI188996.1|CI188996
EST:     CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88483049|gb|CI420320.1|CI420320
EST:     CTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: CTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88847687|gb|CI018378.1|CI018378
EST:     CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88518693|gb|CI446347.1|CI446347
EST:     TTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: TTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
EST: gi|88379776|gb|CI503975.1|CI503975
EST:     CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAG                         TGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC
genomic: CTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGC

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: 53 (upstream exon), 72 (downstream exon)
Score: 11

TCTTTCGTATTTCAAGAGAAGCATATCCATATGAGGACACATCTCAGCTTCTTTCCCGTGTGATCTCTAGCTATGGAGCGAATCGAATAATGTGGGGAAGgtaattcaca ... tattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGCGATCTCTCATGTCGCCGGCAAGATACCTGTTTCCTCGTCAGATTTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgcaaaccccagtacctgtataaacttcttatgctctgcacttattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGCGATCTCTCATGTCGCCGGCAAGATACCTGTTTCCTCGTCAGATTTGGAA
                                           cttattct  CT-rich tract
                     tataaacttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctattagaaatctgtaatggacacgaatagatgatctcttgcatgcttgcaaaccccagtacctgtataaacttcttatgctctgcacttattctgcagTGACTTCCCCTTCGTTGTTCCTGAATGTGGCTACAAAGGGGCCAAGGAGGCGATCTCTCATGTCGCCGGCAAGATACCTGTTTCCTCGTCAGATTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - -tgtaatg
- - - - - - - - - - -acacgaa
- - - - - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - -ttgcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgca