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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA

Basic information

species Oryza sativa
transcript LOC_Os07g31370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 2
gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcatt-atcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
||||| || |   |  | |||||||   ||   |||    | | ||||| ||           || | ||||||||| || |||||| |||   |||||||||| |||||||||||| ||||||||||||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||
gtatggtgac---tactactgcattcatagcctgtt----tgccccttgagatctatggactgttgaccttatgcatgttttattttcttt---gcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcatt--atcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
|||| ||  |   |  | |||||  |||  |    |||    | || | |  |||  | | |  |  | ||||||||   ||| || |||| | |||||||||||||||||||||||| | ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||
gtataattac---tactactgca--tccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgca---tgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 3
---gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttat-gcattttgtatttttttttctgcagG-GATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
   | || |  | ||   |   | |||||    ||   | ||  | || ||          | || ||||||| |  ||| |      | | |  |  |||| || |||||||| |||||| |||| || ||| | ||||||||||| || || ||||| || |||||||||||||  | |||||||||||
ttagcattacaggattcctccat-catttaatattttgtttttaaatcatttccctcacaaaagctttatctttttacatgtctctgatgtgtggcaacagGAGACACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATCGCTTATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 2
-----gtatgatggcatcttttg--ctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
     |||   ||    |||||    |  ||||  | | | || |  || |  |           |  | |||  || |   |||     ||  |||    ||||||||||||||| |||||| |||| || ||| | ||||||||||| || || ||||| || ||||||||||| || | |||||||||||
aagcagtacactgttggctttttatttttatttttattgaattctcttaattttcttcctctcaaaacctttactttttatttttc----ttcatttgtgacagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 2
---gtatgatggcatcttttgctgcatttccagttagttgttcta-ctccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
   || | |   ||  |  ||   ||  | |  ||   || |  |  |  ||     ||  | ||  ||  || |||    |  | |  | |||||  ||||||||||||||| |||||| |||| || ||| | ||||||||||| || || ||||| || || ||||| || |||| |||||||||||
tgggttttagttcaattaatgacacaccttcttttgactggtggagttttttttttttctcccggtgtt-cctaatgttcatcttttcatgttttcgacagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 2
gtatgatggcatcttttgctgcatttc----cagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
||     |     ||||| | || ||     ||     || ||  |||  | | |  |       |    |  ||| ||| || |   | | ||    ||||||||||||||| |||||| |||| || ||| | ||||||||||| ||||| ||||| || || ||||| || |||| |||||||||||
gtgcatcgttgggttttggttcaattaatgacacccctttatttgactggtggagtttttttttcccccctaatattcatctttt-catgtgttatgacagGGATACAGCTGGGCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATCAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
-------gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
       |||  |    | |||||  |   |||  | | | || |  || |  |    |         ||   ||   |  | ||| | |||  |||    ||||||||||||||| |||||| |||| || ||| | ||||||||||| || || ||||| || ||||||||||| || | |||||||||||
ataagcagtac-actatagctttttttttttttttattgaattctcttagttttcttcatctca---acaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
||| |||        |   |  |||| |   || |         | |||   |||         |   | |        |      |  |    ||||||||||||||| || || |||||||||||| | ||||| ||||||||||| || || ||||||||||| || || | |||||||||||
gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 2
gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattat----cttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
  ||||  |    |    ||  ||   || ||  ||  | | || ||   ||    |  | ||||||    |||   |||||  | |||  | || || ||||||||||| || |||||| ||||||||||| | ||||| ||||| || || || || || ||||| ||||| |||| |||||||||||
-gatgagtgtgattgagcctagatgcacaatttattcctatgctactaacgagcatgttgtcattatttctctttgacatttcatttttgctcttatgtagGGATACAGCCGGGCAGGAAAGATTCAGGAGTCTCATTCCGAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
---------gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctg-cagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
         |||  ||  ||| |||||   ||  || | |       ||||     ||   || |  |   ||| |||  | | |||  | ||| |||||||  ||||||||| || || |||||| | ||||||||| |||| ||||| || || || ||||| || ||||| ||||| |||| |||||||||||
aatatttttgtacaatctcatgttttgaaaca--tcaaatcca--agtctataatctgacgatggcta---attgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA

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|58594986|gb|CF993294.1|CF993294
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGGACGGTCAGACTGCAACTTTG                         GGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTGgtatgatggc ... ttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAG




















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: 67 (upstream exon), 75 (downstream exon)
Score: 129

GCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTGgtatgatggc ... ttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA
                                 ttttgtattttttttt  CT-rich tract
                    attatcttatgcattt  TA-rich tract