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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
||| |  ||| ||||  |   |||        | || ||||    || ||||        ||       |||  ||  ||||| ||||  ||||||||||| | |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||
gtatttgccagtcttaggcgttgc------aaagcttttgcaccatactttt--------atgtggctggctaattatatttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 10
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
|||||    | |||| |||  |||  |||||          |||  ||   |||  || |||       |||  ||  ||||  ||||||||||||||||| | |||||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| || ||| |||||||||||||||
gtact---tagtcttatgtgttgc-aaagct---------tttg--aaccatac--atttatatggctggctaattttatttattttgtcagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 10
--gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
      |    | |||| |||  |||  |||||          |||  ||   |||  || |||       |||  ||  ||||  ||||||||||||||||| | |||||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| || ||| |||||||||||    
tcaaggtacttagtcttatgtgttgc-aaagct---------tttg--aaccatac--atttatatggctggctaattttatttattttgTCAGGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCT----

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA14G02530.1 (Glycine max), 3'ss of exon 12
gtactgaccaatcttgtgtactgctgaagc-tgaactattgcttggtaattttactaatatattca-atgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
           | || |  | | ||||||  |  ||||  ||| |||  | |   |   |||| |  ||   ||  ||    |  |  ||| ||||||||||||  ||||| ||| | || || ||||||||||| ||||||||||||||||| || ||||||||||| ||| | || |||||  | |||||||
------gtatgttttcta-attactgaagtatagacta--gctgggttttctctttttgatatcctcatacactttttatggtctccatgttagGCTGCTGTTAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 12
gtactgaccaatcttgtgtactgctgaagc-tgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
           | || |  | | |||||   | |||||  ||| ||   |||  |   |   |||    | ||  ||    |  |  ||| |||||||||| |  ||||| ||| | || || ||||||||||| ||||||||||||||||| || ||||||||||| ||| | || |||||  | |||||||
------gtatgttttcta-attactgaaatataaacta--gctgggc--tttctcctttgatttcctcatactttttatggtctccatgttagGCTGCTGTCAATGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 7
----gtactgaccaatcttgtg-tactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
      ||| ||  || ||  | || |  | |  |    | |  | |   | ||   |  |||| || |  | | ||     | ||  || | ||||||||||||||  || |||||  | |||||| |||| ||||| || ||||| || ||||| |||||||||||||||||||| || |||||| | |||||||
gtatacacttacttatttttcgatattaataatacaatgccagagttaaatgatagcaaaaata-ataccctattctt----cgttatctgtctcagGCTGCTGTTAGCGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 3'ss of exon 6
---gtactgaccaatcttg-tgtactgctgaagctgaactattgcttggtaattttactaatatattcaatg-tgctcgttccatttgctttg----tcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
    | | |  | |  ||  |   ||| ||    |  ||| | | |  | |||  |   | | |||| | ||   | | | |  |||  | ||      |||| ||||| |  |||||| |  |    ||    || ||||| || || ||||| ||||| |||||||||||||||||  ||||||||||  |||||||||
gttttcccgctcgacattcctccgctggtgtttttccactttcggtgtg-aatactgggagtctattgactggctcgcatgcgctttattgtggaatctagGCAGCTGTGAGTGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
gtact-gaccaatcttgtgtactgctgaagctgaact----attgct--tggtaatt--ttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
 | || |     | | |   ||     |  || | ||    ||  ||  |||||||   | |||| || |        | |  |    || | |||  ||||| || || |  |||||  |  |    ||   |||||||||||| |||||||| ||||||||||| ||| |||| || |||||||||||  |||||||||
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggattta-cagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ31629 (Selaginella moellendorffii), 3'ss of exon 6
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
                              |   |      |  ||||||     || |  |||  | ||||     ||   |   | | ||||||||||||  ||  | ||    || ||  |||| || ||||| || || || ||||||||||| ||||||||||| || ||||||||  |||||||||
--------------------------gtattcggcgtggattgcgtaatt----caagagtttctttttgctga---cagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
                         | |   |     | | ||| | | || |  | | | ||   | ||||     ||   |   | | ||||||||||||  ||  | ||    || ||  |||| || ||||| || || || ||||||||||| ||||||||||| || ||||||||  |||||||||
-------------------------gtattcgg--cgtggattgcttaattcaagagtttctt---tttgctga---cagacgtcattttagGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

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|38478516|gb|CF962649.1|CF962649
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|55436812|gb|CV731566.1|CV731566
EST:     ACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: ACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|33794308|gb|CF323041.1|CF323041
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|58613350|gb|CK041062.1|CK041062
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGGCAGG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|25806798|gb|CA762759.1|CA762759
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|11233501|gb|AU164913.1|AU164913
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|5701685|gb|AU062775.2|AU062775
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|55435262|gb|CV730762.1|CV730762
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT
EST: gi|5443721|gb|AU062434.2|AU062434
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTG
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTG
EST: gi|58609985|gb|CK038018.1|CK038018
EST:     TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG                         GCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAGGGCTGTCATTGAT
genomic: TTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGAT

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: 69 (upstream exon), 72 (downstream exon)
Score: 70

GACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAGgtactgacca ... gctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG
              tactaat  putative branch site (score: 70)
                                          tttgcttt  putative PPT
        taattttactaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgaccaatcttgtgtactgctgaagctgaactattgcttggtaattttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT