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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtggtataataacatggtttagtaataccctatcttctaacatatttggtactgctgcaatttattcgttctgaatcattctgcaacatttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G060977_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------atgtggtataataacatggtttagtaataccctatct---tctaacatatttggtactgctgcaatttattcgttctgaatca---ttctgcaacatt-------tttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG
                                            ||| | |||||||  |  ||  || || |  | | |   |  ||   || ||   ||| |  |   |   | ||   ||| |   ||||| | || |         ||||||||||||||||| || ||||||||||| || | ||| ||  ||||||||||| |||| ||||| |||
gtagtagaataatgaagataatccttcattttctccacgcatgctgttgcataataaattatttgtgtcattcaatctttaactggaatccatatgcagctgttttatggtgcccatttcaaatgagttttctgaatcactgcattatcctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAGGTAGCTACTCCAAAG

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G030902_T03 (Zea mays), 3'ss of exon 5
-------------------------------------------atgtggtataataacatg---gtttagtaataccctatcttctaacatatttggtactgct-----gcaatttattcg--------ttctgaatcattctgcaacatttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG
                                           || | | |||||||  |    || ||||   | | |    |  ||   || ||   ||||      |    | ||||         |||||| ||| |     |   || ||||||||||||||||| || ||||||||||| || | ||| ||  |||||||||||||||| ||||| |||
gttgtaaaataatgaagataacttttcattttctccatgcatgatattgcataataaattctgtgtatagttcaatctttaacttaaatccatatgcagctgccttatagtgcctaattcagattagttttctgattcactgcattattattctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAGATAGCTACTCCAAAG
















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|117251528|gb|CT844202.1|CT844202
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|33682634|gb|CF310873.1|CF310873
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|66924263|gb|CX111111.1|CX111111
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCT
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCT
EST: gi|8857838|gb|AU095156.1|AU095156
EST:     ATCTCGTGGGGTTTGGT-ATGGNACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGA
genomic: ATCTCGTGGG-TTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGA
EST: gi|88430193|gb|CI565206.1|CI565206
EST:     GATCTCGTGGGTTTGGTTATGTAACGT-CTCATCAGGTGATGATGC-AAC                         AATGTTCTTGAGTGTGAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAG
EST: gi|58672423|gb|CK061109.1|CK061109
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTACTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|58676983|gb|CK065670.1|CK065670
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|33676567|gb|CF304806.1|CF304806
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCT
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCT
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|58672650|gb|CK061336.1|CK061336
EST:     GATCTCGTGGGTTNGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|58676963|gb|CK065650.1|CK065650
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|58591906|gb|CF990214.1|CF990214
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|33800393|gb|CF326065.1|CF326065
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|33795605|gb|CF323672.1|CF323672
EST:     ATCTCGTGGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACT
genomic: ATCTCGTGGG-TTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACT
EST: gi|33684319|gb|CF312558.1|CF312558
EST:     ATCTCGTGNGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: ATCTCGTG-GGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
EST: gi|86596647|gb|CI286560.1|CI286560
EST:     GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG                         AATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAG

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: 67 (upstream exon), 65 (downstream exon)
Score: 15

GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcc ... tttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtactgctgcaatttattcgttctgaatcattctgcaacatttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG
                                           catttttttc  CT-rich tract
                                         aacattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtggtataataacatggtttagtaataccctatcttctaacatatttggtactgctgcaatttattcgttctgaatcattctgcaacatttttttcagAATGTTCTTGAGTGTGAGCATGTTCTCGGAAACCGAACTCTAGAAGTGAAGATAGCCACTCCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - -aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgca