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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatatgtacttcacgctgccgacacagttgatattattgacatcatttttcagtccttttacaaagtactcctgtgtttctcttatgaaccgtggttttgaatgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGAGTGAAGTCGATCTGGAGAGAGGAGTCTACTCACCACATTCAAGTGAGGA

Basic information

species Oryza sativa
transcript LOC_Os10g42100.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G033526_T01 (Zea mays), 3'ss of exon 11
--------------------gtaagcatatgtacttcacgctgccgacacagttgatat---tattgacatcatttttcagtccttttacaaagtactcctgtgtttctcttatgaaccgtggttttgaatgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGAGTGAAGTCGATCTGGAGAGAGGAGTCTACTCACCACATTCAAGTGAGGA
                    ||     ||   || |   || | |    ||   ||||     ||     |  |  || | |  |||  |    |  |  | | |||  || || |  ||||| || |||||||  |||||| || ||||  |||||  | || |||||||| || ||||||||||| |||||||  || |||||||||||||| || ||||||||||| ||||||||||
gtaagaccatgtgctgtgaagttccattactgaccttttgcagtcagttcatcagataaacacatctctgttttacttgaatattttgcccttttgttattatattttactgattattcgtggattggaatgttgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACCACATCCAAGTGAGGA

upper sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 11
----------------gtaagcatatgtacttcacgctgccgacacagttgatattattgaca----tcatttttcagtccttttacaaagtactcctgtgtttctcttatgaaccgtggtt------ttgaatgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGAGTGAAGTCGATCTGGAGAGAGGAGTCTACTCACCACATTCAAGTGAGGA
                || |   |       | |   |    |  ||||| ||   ||  |||    ||   |||   |  | ||     |  || | || ||| | || | |    |  ||      ||||||| |  |||||| || ||||  |||||  | || |||||||| || ||||||||||| |||||||  || |||||||||||||| || |||||| |||| ||||||||||
gtaaggccattgtgctgtgaagtttcactgctgatcttttgcagtcagttcatcagataaacacatctcggctttacttgatctttttttgctcttccgtttttttattttaactgattattcatggattgaatgctgaacagAAAGCACAATATGTGAAGAAGGGAGACTACGTCACTCTTGTTCAGAGCGGAGTGACTTCAATCTGGAGAGAGGAATCCACTCACAACATCCAAGTGAGGA
















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|58676860|gb|CK065547.1|CK065547
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88473007|gb|CI410278.1|CI410278
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|29661411|gb|CB657686.1|CB657686
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88436808|gb|CI521559.1|CI521559
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|29614922|gb|CB619935.1|CB619935
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88477158|gb|CI414429.1|CI414429
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88271415|gb|CI387468.1|CI387468
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTTTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|58691037|gb|CK079724.1|CK079724
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|58660571|gb|CK049251.1|CK049251
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88451187|gb|CI534180.1|CI534180
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCNTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|58677681|gb|CK066368.1|CK066368
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88520722|gb|CI446378.1|CI446378
EST:     TTCTGATGATGCAGA-GANAACTTTCTCTAGAGCAATTAGTAGCTTNCTG                         AACGCCCAATTCGTGAAAGAAGGGGAGTACGTGACCCTTGTTCAGAGTGGA
genomic: TTCTGATGATGCAGAGGA-AACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88272849|gb|CI386109.1|CI386109
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|58666184|gb|CK054870.1|CK054870
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88440386|gb|CI549267.1|CI549267
EST:     TTTCTNATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|22307162|gb|BQ908384.1|BQ908384
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGC-ATTAGTAGCTTGCTG                         AACGCCC-ATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88489512|gb|CI426784.1|CI426784
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|86519992|gb|CI160198.1|CI160198
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88322594|gb|CI542922.1|CI542922
EST:     TTTCTGATAATGCAGAGGAAACTTTCTGTAGAGCAATTAGTAGCTTGCTG                         AACNCCCAATTCGTGGAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|218497937|gb|FG958969.1|FG958969
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTTAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|29628928|gb|CB633939.1|CB633939
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88478930|gb|CI416201.1|CI416201
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|86602847|gb|CI357211.1|CI357211
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|89198679|gb|CI016764.1|CI016764
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
EST: gi|88835790|gb|CI370895.1|CI370895
EST:     TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTG                         AACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA
genomic: TTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGA

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), 75 (downstream exon)
Score: 39

GAAGCAACGTCTGGCACTCTACCAGGGTGTGGTTCCCATTTACATGAAGTTTTCTGATGATGCAGAGGAAACTTTCTCTAGAGCAATTAGTAGCTTGCTGgtaagcatat ... tgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGAGTGAAGTCGATCTGGAGAGAGGAGTCTACTCACCACATTCAAGTGAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacaaagtactcctgtgtttctcttatgaaccgtggttttgaatgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGAGTGAAGTCGATCTGGAGAGAGGAGTCTACTCACCACATTCAAGTGAGGA
                                      ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatatgtacttcacgctgccgacacagttgatattattgacatcatttttcagtccttttacaaagtactcctgtgtttctcttatgaaccgtggttttgaatgtttgacagAACGCCCAATTCGTGAAAGAAGGGGACTACGTGACCCTTGTTCAGAGTGGAGTGAAGTCGATCTGGAGAGAGGAGTCTACTCACCACATTCAAGTGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG