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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccctctcattcccctcctcagtcccatctactactactaattacaacaagggagtagttattattattaagctttcaattgctgttagcctgc...

Basic information

species Oryza sativa
transcript LOC_Os05g01560.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G893252_T01 (Zea mays), 5'ss of exon 2
TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccct--ccctctcattcccctcctcagtccc---atctactactactaatt-acaacaagggagtagttattattattaagctttcaatt-gctgttagcctgc
|||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| |||||||||||||||||||||||||| ||||||||||| ||||||  |    |||| ||| |  |   ||  |     |  |     | |||||| |     |||||  |   | | |    | ||||  |    ||  ||       
TCTTCGACGGCTACGCGCACCTCTCCTCCGGACTCGCCTGCGGCCTCGCTGGCCTCGCTGCCGGCATGGCCATCGGCATCGTCGGAGACGCCGGAGTTAGgtactgtaatactctgattgcagttgccatcctttgtacatgtccatgctaattgattctcagggaaaaaaaactgtcgccaggcttagaccaagcaatt-------

upper sequence: LOC_Os05g01560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA11G07980.1 (Glycine max), 5'ss of exon 1
TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccctctcattcccctcctcagtcccatcta--ctactactaattacaacaagggagtagttattattattaagctttcaattgctgttagcctgc
|||||||||| ||||| |||||||||||||| ||||| ||||||||||| || ||| |||| ||||||||||| ||||| || ||||| ||||| || |||||  ||| |||   |||   |  ||  |  | | |    ||  ||    |  || |||       |  |||| ||||   | |    |   |||||     
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCGCTTGCGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGATGCCGGTGTTAGgtattctcactcattttctatttttctttttctttttacttataacatgatcgaataagatgcgtatagttataattattttcttgcgtatggttaggta--

upper sequence: LOC_Os05g01560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G05630.1 (Glycine max), 5'ss of exon 2
TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccctctcattcccctcctcagtcccatc--tactactactaattacaacaagggagtagttattattattaagctttcaattgctgttagcctgc
|||| ||||||||||| |||||||| || |||||||| || |||||||| || ||| |||| |||||||||||||||||||| ||||| ||||| || |||||  |  | |   | | |  ||     ||   |   | || || ||   | |    |   |     | | |||  |  |||      |  ||| |  |   
TCTTTGACGGTTACGCGCACCTCTCTTCGGGTCTCGCTTGTGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatcattcaaattcaatcaagcttcgagttgttgctgctgctttatgctttcactaatgctgtttgattgatgtgctggtgtgttttgtaattca--

upper sequence: LOC_Os05g01560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G24220.1 (Glycine max), 5'ss of exon 2
TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccctctcattcccctcctcagtcccatctactactactaattacaacaagggagtagttattattattaagctttcaattg-ctgttagcctgc--
| || ||||| |||||||||||||| || |||||||| || |||||||| || ||| |||| |||||||||||||||||||| ||||| ||||| || |||||  |  | | | | |    || |   | | |  || |  | ||  |       | |   |  ||| | ||       | |   |||  || | |  ||   
TTTTTGACGGCTACGCCCACCTCTCTTCAGGTCTCGCTTGTGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatcatttaaatttaatcat-gcttcgagttattgttgctgctgct--ttatgttttcattaatgttgcatgcttgttgtttggttgatgggttgagt

upper sequence: LOC_Os05g01560.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA01G37320.1 (Glycine max), 5'ss of exon 1
TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccctctcattcccctc-ctcagtcccatctactactactaattacaacaagggagtagttattattattaagcttt-caattgctgttagcctgc
|||||||||| ||||| |||||||||||||| ||| | ||||| || || || ||| |||| ||||||||||| ||||| || ||||||||||| || |||||  ||| |||   |||  ||| |||  |  | |     |    |   |  |   |   | || ||  |   ||   | ||   | ||| |   || |   
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCTCTTGCGGTCTTGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGACGCCGGTGTTAGgtattctcactccttttctactctctctttttctttcgaaaaagatgcgtgtagttata-attattttcttgcatatggtttggtatttggttcaaggcca-

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|88208510|gb|CI208359.1|CI208359
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|86532508|gb|CI172714.1|CI172714
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88480668|gb|CI417939.1|CI417939
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|38473664|gb|CF957796.1|CF957796
EST:     GTACTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAN                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GT-CTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88509401|gb|CI436907.1|CI436907
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCANCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|33660490|gb|CF291457.1|CF291457
EST:     GTCTCGCCGCCGGCATGGCCATCGGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGTGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GTCTCGCCGCCGGCATGGCCATC-GGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88480063|gb|CI417334.1|CI417334
EST:     CGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: CGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|29686032|gb|CB682307.1|CB682307
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|25799453|gb|CA755414.1|CA755414
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|86601472|gb|CI253800.1|CI253800
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88282552|gb|CI403948.1|CI403948
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88226731|gb|CI224716.1|CI224716
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|38474557|gb|CF958690.1|CF958690
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAG
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAG
EST: gi|88537736|gb|CI466709.1|CI466709
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88240943|gb|CI240792.1|CI240792
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88212647|gb|CI212287.1|CI212287
EST:     GGTCTCGCCGCCGGCATGGCNATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|86420321|gb|CI056310.1|CI056310
EST:     GCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|88538246|gb|CI467260.1|CI467260
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|33660491|gb|CF291458.1|CF291458
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGTGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
EST: gi|27578035|gb|CB000730.1|CB000730
EST:     GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAG                         GGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT
genomic: GGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTAT

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: 49 (upstream exon), 29 (downstream exon)
Score: 4

TCTTCGACGGTTACGCCCACCTCTCCTCCGGTCTCGCCTGCGGCCTCGCCGGTCTCGCCGCCGGCATGGCCATCGGCATCGTCGGCGACGCCGGAGTCAGgtaccctccc ... tcctctgcagGGCCAATGCGCAGCAGCCAAAGTTGTTCGTGGGCATGATCCTCATCCTTATCTTTGCAGAAGCTCTTGCTCTGTATGGCCTGATTGTTGGTATCATCCTC




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