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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA

Basic information

species Oryza sativa
transcript LOC_Os10g32970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G022019_T01 (Zea mays), 3'ss of exon 2
gtacatttcctctaaaatcattgcttagt-ttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatc-----atttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA
              | ||| ||| |  || || |||      | |||  || |    ||  | | ||||   |  ||  | | |   | |  ||||||      | | |   |||| || | || |||||||||| |||||||||| ||||| ||||||||||||||||  ||||| ||||||||| ||||||||||||||||    |||||||| ||||| ||||| |||||||
------------gtacatccttgttgtgtatttgtcta----tttgatttgttcaaaatcgagcgtctgcaaccagatgtttttctgagatgttctattgatggactgcctttgactaattgtttgaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA

upper sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCA------GAGAGGAGACAAGCTTGCATTGTGGACTA
                     |  |   ||    |     | || |    ||||   | |    |||||   |||    ||  | |   ||||   | | |  | ||    |  | ||   | ||| || |||||||| ||||||||||||| |||||||||   || || |||||||| || |||||||||||||| |       ||    |||||||||  | ||||      
--------------------gtattacattctaaccctaaccctaa---ccttttactct----tctgtgttttgttagatgatatgtggttttggtgactggttct----atttcttatgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGTGTGGTTGCTAGTGTCCGTCCACAGTCGAAGCAAGACAAGCTCTCCTTGT------

upper sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S426_46V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------gtacatttcctc-taaaatcattgc---ttagtttggtcggaggctctga--agtgctttggatataacatctgttgcttgacctatcttctaaagtttctatc---atttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA
                                                 | | || ||||| |  ||  |  |    || ||    |     |||   |  || |||  | ||||   |  |  |  |    | |||   | |  | |  ||    | |  |  |         || |    | ||| || ||||| ||||||||||||| ||||| ||| |||| |||||||| |||| |||||  || ||  |   |  |  ||| ||| ||||  | ||||| |
gtactgtctatctttcttgattctgggttttcctactgtcgctttggttgaatatgtcctcatggaaatagggaaagttggtcaacttttgagctgaaacaagcgctccgcatatctgagatagttttgattcgatcaattgatatctagatttgaagtcttattatattgtaatttgtgggttcagTTGCTGGCTATGATTGGAGAGCAATTTGACGAAGGTGATGAAATTTGCGGAGCTGTTGTGAGCGTAAGGAGGGCACAAGATAAGATTGCCATCTGGACGA

upper sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S39_197V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatt-tctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA
                       |||  | |  ||| |   | |    ||   || || || ||   ||  |  ||    |  | |    |  |||  ||   ||| | |  | |   | |   |||||| || ||||| ||||||||||||| ||||||||| |||| |||||||||||||  ||||  || ||  | |        |||||  | ||  | |||||||
-----------------------ctt--tctcatcgtaactttttgtatgtactgaatgtagca---gtgacgagattagtactattgt-tgcctacgataacctggtaatcatcacct-gtggatgcagTTGCTGGCTATGATTGGAGAGCAATTTGATGAAGGTGACGAAATTTGTGGAGCAGTTGTCAGCGTGAGACGAGCGCAGGACAAAATAGCTATCTGGACTA

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|86522564|gb|CI162770.1|CI162770
EST:     ATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: ATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|8860119|gb|AU097437.1|AU097437
EST:     CAGGAAGACCACCCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CAGGAAGACCA-CCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|89165097|gb|CI255154.1|CI255154
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|86525895|gb|CI166101.1|CI166101
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCCTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|218493197|gb|FG958056.1|FG958056
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|89161806|gb|CI102154.1|CI102154
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|218485786|gb|FG945172.1|FG945172
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         TTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|86501861|gb|CI144494.1|CI144494
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|27576343|gb|CA999037.1|CA999037
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|29665281|gb|CB661556.1|CB661556
EST:     CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: CTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|218483813|gb|FG965939.1|FG965939
EST:     TGTGCCATGTTGCAGGTAGACCACCCTTGTAGAACATGTGGCTTGTAACG                         CTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: TGTGCCATGTAGCAGGAAGACCACCCTTG-AGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
EST: gi|86507489|gb|CI150122.1|CI150122
EST:     AGAACATGTGGCTTGAAACG                         CTGATGGCTCTGATTGAAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA
genomic: AGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGA

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), 71 (downstream exon)
Score: 57

TGTAGAACCAAAGTGGGAAGACCCAGAGTGTGCAAATGGGGGCAAATGGACTGTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcc ... gaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctatcttctaaagtttctatcatttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA
                             tgctgac  putative branch site (score: 57)
                                       cttttcg  putative PPT
           taaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT