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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaataacttcttcagtactgtattcatcaatttattagcctgatttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 3
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 3
lower sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 3
ttaaataacttcttcagtactg-----tattcatcaatttattagcctgatttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG
     |   || || |  | ||      |   |||||  | || |  |  ||   |  | ||  | || | | ||| | || ||||||| |    ||||| | ||||||| || ||||| ||||||||||||||||| |||||||| ||| ||||||| || ||||| |||
-----tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G030902_T04 (Zea mays), 3'ss of exon 3
ttaaataacttcttcagtactg-----tattcatcaatttattagcctgatttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG----------------------------------
     |   || || |  | ||      |   |||||  | || |  |  ||   |  | ||  | || | | ||| | || ||||||| |    ||||| | ||||||| || ||||| ||||||||||||||||| |||||||| ||| ||||||| || ||||| |||                                  
-----tcgttttttgaacattggcatgcaactatcaacatttttgtgtatttattttctgtgcatgcttatttacctccatgtttcttgcataccaaaataacagGAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGGTTGTAAAATAATGAAGATAACTTTTCATTTTCT
















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:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|33682634|gb|CF310873.1|CF310873
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|66924263|gb|CX111111.1|CX111111
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|8857838|gb|AU095156.1|AU095156
EST:     AGAGTACATGGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGGTCGATCTCGTGGGGTTTGGT-ATGGNACGTTCTCAT
genomic: AGAGTACATGGG-CAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGG-TCGATCTCGTGGG-TTTGGTTATGTAACGTTCTCAT
EST: gi|88370619|gb|CI590197.1|CI590197
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTC
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTC
EST: gi|88431461|gb|CI579578.1|CI579578
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTA
EST: gi|88356835|gb|CI619321.1|CI619321
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTACATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|88430193|gb|CI565206.1|CI565206
EST:     GAGAGT-CATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGT-CTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|88351304|gb|CI627320.1|CI627320
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAA
EST: gi|58672423|gb|CK061109.1|CK061109
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|58676983|gb|CK065670.1|CK065670
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|88425369|gb|CI567089.1|CI567089
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTACATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGAT
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGAT
EST: gi|33676567|gb|CF304806.1|CF304806
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|88377696|gb|CI605531.1|CI605531
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     ACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: ACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|58672650|gb|CK061336.1|CK061336
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTNGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|2312757|gb|C28912.1|C28912
EST:     GAGAGTACATGGGCAAGTTTNGACCCCTAGATGATTGCNTCGTCATGAAG                         -AGCGTTCGTCTGGTCGATCTCGTNGGGTT-GGTTATGTAACGTTCTAATC
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGT-GGGTTTGGTTATGTAACGTTCTCATC
EST: gi|58676963|gb|CK065650.1|CK065650
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|58591906|gb|CF990214.1|CF990214
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|33800393|gb|CF326065.1|CF326065
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|58664289|gb|CK052975.1|CK052975
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTATGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
EST: gi|33795605|gb|CF323672.1|CF323672
EST:     AGAGTACATGNGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGGTTTGGTTATGTAACGTTCTCATC
genomic: AGAGTACATG-GGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGG-TTTGGTTATGTAACGTTCTCATC
EST: gi|88414769|gb|CI604127.1|CI604127
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGG
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGG
EST: gi|88368494|gb|CI572703.1|CI572703
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTC
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTC
EST: gi|33684319|gb|CF312558.1|CF312558
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGNGGTTTGGTTATGTAACGTTCTCATC
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTG-GGTTTGGTTATGTAACGTTCTCATC
EST: gi|86596647|gb|CI286560.1|CI286560
EST:     GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG                         GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA
genomic: GAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCA

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: 71 (upstream exon), 70 (downstream exon)
Score: 41

GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAGgtttgtagca ... aaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG
                                       tacgttaaaattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaataacttcttcagtactgtattcatcaatttattagcctgatttggtaatttgtgtactgactgaccactatctttcttgtacgttaaaattatagGAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- aaataac
- - - - - - - - - - - - - - - - - - - -gcctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgactg