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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctagctctaatttctttgaaggcgagaagattaacctcattcgaattgtgacattcctttctcattccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g60200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G309840_T01 (Zea mays), 3'ss of exon 2
--------gtattctagctctaatttctttgaaggcgagaaga---ttaacctcattcgaat-tgtgacattcctttctcattccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG
        |||| |||  ||  | ||   | | ||| | ||||   | || ||  |  |||| |||     | |  ||| || |  | ||  ||||||||||||||||| |||||||||||||| ||  | ||| |  | |||||||||||||||||||||| |||||||||
caagacatgtatgctaagtc-gactttggtaatggctaaaagaaattgaatcttctgtgaatctgttctgatgccatcttatccacaacaaaacttacaagGTGTTTGATTTGAAAAACTACACATTACTTTATTCGGTGTCTGATAAGAATGTTCAAGAAACAAAGATCAG

upper sequence: LOC_Os01g60200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0056g00230.t01 (Vitis vinifera), 3'ss of exon 4
------------gtattctagctctaatttctttgaaggcgagaagattaacctcatt-cgaattgtgacattcctttctcattccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG
             |  |     |   ||     ||    | | | |  ||   | |||   |||  | |||||  ||| |  ||      || |  ||||| ||||||||| ||||||||||   | |||||||  | ||||||||| | ||||| |||||||||||||| ||
gtatatctttaattgcttgtattgctatactcatggtcaccaaatgcatattttaattgttaatcctaacattgtttttt--tttttgttagCATATACAAAGTGTTTGACCTGAAAAACTATGTTATGTTGTACTCTATATCTGATGAAAATGTGCAAGAAATAAAGATAAG

upper sequence: LOC_Os01g60200.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0067g00100.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtattctagctctaatttctttgaaggcgagaagattaacctcattcg-aattgtgacattcctttct-cattccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG
                     | || |    |   |  || ||||     |  |   |   |  |||   ||| ||| | |   || |   || | |  || |  |||||||| |||||| |||||||||| ||  |||||||  | ||||| |||||  ||||||||||||| ||||||||
gtaaatattaagctatttctctgtttttatgcacttggctatgaatatttggtgtgcagttttcttcttgattctgatactttattttgtttttccattagCATATACAAGGTCTTTGACCTGAAAAACTATACAATGTTGTACTCCATATCAGATAAACATGTTCAAGAAATCAAGATCAG

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|58689201|gb|CK077888.1|CK077888
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|218505419|gb|FG959318.1|FG959318
EST:     GAATTCGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|58678194|gb|CK066881.1|CK066881
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|44671831|gb|CR285265.1|CR285265
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|58596250|gb|CK006778.1|CK006778
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|218480439|gb|FG952420.1|FG952420
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|58599623|gb|CK010151.1|CK010151
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|218500120|gb|FG948314.1|FG948314
EST:     GAA-TTGATGATG-TAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATC
EST: gi|58694838|gb|CK083525.1|CK083525
EST:     GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAG                         TACTTACAAGGTGTTTGA
genomic: GAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGA

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: 72 (upstream exon), 72 (downstream exon)
Score: 23

CTGGTTTCCCTCTTTTCGAGACAGAGTCCTTGAAATGGCCAGGTTTTGTGGAATTTGATGATGTTAACGGGAAGGTGCTGACTTATTCTGCCCAAGACAGgtattctagc ... ttccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcgagaagattaacctcattcgaattgtgacattcctttctcattccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG
         gattaac  putative branch site (score: 23)
                                cattcctttctcattc  putative PPT
       aagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctagctctaatttctttgaaggcgagaagattaacctcattcgaattgtgacattcctttctcattccaaccagTACTTACAAGGTGTTTGACTTGAAAAACTACACTTTGTTGTATACAATATCTGATAAGAATGTTCAAGAAATAAAGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA