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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttcaccttgttggttgtgaatttatatattactggactaccgcactaatacgagttttctcacag

Basic information

species Oryza sativa
transcript LOC_Os01g50760.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 7
GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttcaccttgttggttgtgaatttatatat--------tactggactaccgc-actaatacgagttttctcacag
||||||||||| ||||||||  |||||||||| ||||| ||||| | |||||| ||||||||||| || |||||||| |||||||| ||||||||||||    |     || ||    |  || | | ||          || ||| ||||| |   | ||  |  ||||   ||||
GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctcttgtttttttaaggccaaatgacatggatttgctatattgggctacctctgatcattggcatttttctacag

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 7
GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttcaccttgttggttgtgaatttatatat--------tactggactaccgc--actaatacgagttttctcacag
||||||||||| ||||||||  |||||||||| ||||||||||| || ||||| |||||||||||||| |||||||| |||||||| ||||||||||||    ||    ||  ||   |  || | ||||          || ||||||||| |  | || ||  | ||||||  |||
GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttttctgaaggctaaatgatatggatttgctgtattggactacctctgattactattatttttct-gcag

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 8
GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgta---ccttttcac--------cttgttggttgt-----gaatttatatat-tactggactaccgcactaatacgagttttctcacag------------------------
||||||||||| |||||  |  | |||||| || | || ||    | |||||| |||||||||||||| || ||||| |||||||| ||||| ||||||   | || | |         | | |||| | |     ||  | || ||    || || | | | | ||  ||   | || |  |                          
GTTGCATGTGCATTGCTTATGGCGGGTGAGGATCTAGACAAAAATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAGgtaatactttgttataggtttgacctcttggctttctttagagatcatttagactctagaatgctgtattataacctatcttttttctctttccttttcccctctcattttag

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA04G34770.1 (Glycine max), 5'ss of exon 1
----------GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgta---ccttttcac--------cttgttggttgtgaatttatatattactggactaccgcactaatacgagttttctcacag---------------------------------------------------------------------
          ||  ||| ||| |||||  |    |||||| || | || ||    | |||||| |||||||||||||| || ||||| |||||||| ||||| ||| ||   | || | |         | | |||| | |   |||| | || | |      |   | |  |    || |    |  |                                                                     
CCTTACACAGGTGACATATGCATTGCTTATGGTGGGTGAGGATCTAGACAAAAATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAgtacagataatactttgttataggtttgacctcttggctttc--tttagagatcatttagaccctagaatgttgtatgtctatatattgcccttatgagcttgaaatattttattataacctatcttttttctctttccttttcccctctcattttag

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 8
GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttcaccttgttggttgtgaatttatatattactggactaccgcactaatacgagttttctcacag---------------------------------------------------------------------------------------------
||||||||||| |||||  |  | |||||| || | || |||   | |||||| |||||||||||||| || ||||| |||||||| ||||| ||||||    ||    || | ||||     | |     ||  |     | |    | |  | ||  | ||  | |                                                                                             
GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAGgtaatactttg--ttataggtttgacctcttggctttctttagagatccttttgactctagaatgctgtctgtatgtctacatattgccctcatcagctataaatattttttaaaaactgtattataacctatcttttctctatccttttcccctctcattttag

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|88965695|gb|CI006596.1|CI006596
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|88690724|gb|CI734803.1|CI734803
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|27577652|gb|CB000347.1|CB000347
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|86419076|gb|CI053877.1|CI053877
EST:     ATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: ATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|27576092|gb|CA998786.1|CA998786
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|33820604|gb|CF336113.1|CF336113
EST:     TGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: TGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|87011492|gb|CI279401.1|CI279401
EST:     TGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: TGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|33822342|gb|CF336983.1|CF336983
EST:     AATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: AATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|86535251|gb|CI175457.1|CI175457
EST:     AATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: AATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|29620886|gb|CB625897.1|CB625897
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATTTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|86527820|gb|CI168026.1|CI168026
EST:     GGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|86252127|gb|CI055864.1|CI055864
EST:     TCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: TCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|29684521|gb|CB680796.1|CB680796
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAA                         GATGATTATCTAGATTGTTAT
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTAT
EST: gi|8856728|gb|AU094046.1|AU094046
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|88974804|gb|CI023100.1|CI023100
EST:     TTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: TTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|29688203|gb|CB684478.1|CB684478
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|27554346|gb|CA998246.1|CA998246
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|58681411|gb|CK070098.1|CK070098
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|86521107|gb|CI161313.1|CI161313
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
EST: gi|29684202|gb|CB680477.1|CB680477
EST:     GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAG                         GATGATTATTTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
genomic: GTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG

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: 47 (upstream exon), 45 (downstream exon)
Score: 87

GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttc ... tttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttcaccttgttggttgtgaatttatatattactggactaccgcactaatacgagttttctcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC