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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctactatgattaatgagtgatattaaagctgactagttgcctctttgcctttctgaactgaagttgaccagttcttatatactaattccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT

Basic information

species Oryza sativa
transcript LOC_Os08g01180.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G451366_T03 (Zea mays), 3'ss of exon 10
tagctactatgattaat-gagtgatattaaagctgactagttgcctctt---tgcctttctgaactgaagttgaccagttcttatatactaattccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT
||      | ||||  | |  ||||  |           | |||        ||    |   ||   || |  ||  | |        ||  | |   ||||||||||||||||||||| | | ||| | |||||| ||||||||||| ||||| ||||| ||||||||||| |||| |||| ||| |||||||||||||||||
tacagtgcacgatttgttgtttgattgtggcatcatactgctgctataaaaatgatgcttgaaaactaaatctactggctgcct----cttgtccttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAATAGCAGCTTAGCCATCAATCCTCGCTACGTCCGGTCCTGGTTGGATCTTT

upper sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G021784_T01 (Zea mays), 3'ss of exon 10
--tagctactatga--ttaatgagtgatattaaagctgactagttgcctctttgcctttctgaactgaagttgaccagttcttatatactaattccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT
   ||  | |  |   ||      | |||||  |          | ||    ||    |   ||   ||||  ||  | |     || ||    |  ||||||||||| |||||||||||| || |||| ||| || ||||||||||| ||||| ||||| |||||||| || |||||||| |||| ||||||||||||||| |
tgaagtcattgggggcttggatcatcatattgcattattgctactaccaaaatgatgattgaaaactaagtctactggctgcctcatgct----ctttttacagAGACGCATCTATGGACTGAAGGGAAGGAACATAGATGTTTTTGCAGAGAATAGCAGCTTAGCCATTAATCCTCACTATATCCGGTCCTGGTTGGATCTGT
















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|86854636|gb|CI258929.1|CI258929
EST:     TGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: TGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|58595441|gb|CK005969.1|CK005969
EST:     ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|3760363|gb|C97617.1|C97617
EST:     TGCTGATTCAGTAATTAGAACTGTCAGATTAGTTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: TGCTGAGTCAGTAATTAGAACTGTCAGATTAG-TTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|218494749|gb|FG957718.1|FG957718
EST:     ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|38476686|gb|CF960819.1|CF960819
EST:     ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGTGGAGAAC
genomic: ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|88262193|gb|CI365769.1|CI365769
EST:     ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGAC
genomic: ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGAC
EST: gi|86854626|gb|CI258919.1|CI258919
EST:     TGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: TGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|29627355|gb|CB632366.1|CB632366
EST:     TGCTGAGTCAGTAATTTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: TGCTGAGTCAGTAA-TTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|29613550|gb|CB618563.1|CB618563
EST:     ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|58606681|gb|CK034714.1|CK034714
EST:     ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCG                         AGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGTGGAGAAC
genomic: ATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
EST: gi|86887659|gb|CI311942.1|CI311942
EST:     TGCTGAGTCAGTAATTAAGAACTGTCAGATTAGTTTTTGAAAGTCTTGCG                         AGACACATNTATGGATTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC
genomic: TGCTGAGTCAGTAATT-AGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAAC

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: 57 (upstream exon), 67 (downstream exon)
Score: 22

AGAATCAGCAGATGCTGAGTCAGTAATTAGAACTGTCAGATTAGTTTCTGAAAGTCTTGCGgtaagctaaa ... ccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgcctttctgaactgaagttgaccagttcttatatactaattccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT
                                     tactaat  putative branch site (score: 22)
                                           ttccattt  CT-rich tract
                             ttcttatatactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctactatgattaatgagtgatattaaagctgactagttgcctctttgcctttctgaactgaagttgaccagttcttatatactaattccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT

-agctact