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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcattcatctgtctttcatactgatgtaaattctattcgatgcatttttttttccagttcaatatgtttctgatgcacttctgtgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG

Basic information

species Oryza sativa
transcript LOC_Os10g41590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G341271_T03 (Zea mays), 3'ss of exon 3
gttcattcatctgtctttcatactgatgtaaattctattcgatgcatttttttttccagttcaatatgtttctgat-gcacttctgtgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG
|||| ||| | ||  | | |||   |   || |||| |   ||| |  ||   ||||| | ||| |||||||| ||      | |||  ||||||||||||||||||||| || |||||||| || || ||||||||||||||  |   ||||||||| ||||| ||||||||| | |||||||
gttccttcctttgcgtctgatatgaa---aatttctgt---atggacctt---ttccactccaacatgtttctcattatggctatgtatattatagCTGATTGATGATTTGGTTCTGCTTGGAGTACGGGCTGGTGGGGATTTGGATAATTTGCAAGCACTTGACCATGAAGAGTTATCAGAAG
















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|88336575|gb|CI656846.1|CI656846
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88424216|gb|CI581771.1|CI581771
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88728249|gb|CI751759.1|CI751759
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88296461|gb|CI669237.1|CI669237
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88454307|gb|CI569879.1|CI569879
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88317188|gb|CI626831.1|CI626831
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88309663|gb|CI656404.1|CI656404
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88407459|gb|CI586300.1|CI586300
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88403667|gb|CI575551.1|CI575551
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGGTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88400700|gb|CI596121.1|CI596121
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAG
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88316061|gb|CI618937.1|CI618937
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGGTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88431474|gb|CI579591.1|CI579591
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88729990|gb|CI753605.1|CI753605
EST:     AATGTCCTTACGACAATACATCGATTTGTTTGAATAAAATGTGGAATCAG                         NTGATTGATGATTTACTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|58669159|gb|CK057845.1|CK057845
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88394940|gb|CI607667.1|CI607667
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
EST: gi|88336123|gb|CI647317.1|CI647317
EST:     AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAG                         CTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC
genomic: AATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAAC

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: 70 (upstream exon), 69 (downstream exon)
Score: 25

GTCCAAAATGCGTGCATTGGAAGGCAAGTTCAAGGAGCTGAGGGATGAGCAATGTTCTTACGACAATACATTGATTTGTTTGAATAAAATGTGGAATCAGgttcattcat ... tgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcatttttttttccagttcaatatgtttctgatgcacttctgtgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG
                             ttctgat  putative branch site (score: 25)
                                       cttctgt  putative PPT
     attttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcattcatctgtctttcatactgatgtaaattctattcgatgcatttttttttccagttcaatatgtttctgatgcacttctgtgaattatagCTGATTGATGATTTAGTGCTGCTTGGGGTTCGAGCTGGTGGGGATTTAAACGGTTTGCAAGCGCTTGATCATGAAGAGATGTCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG