Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTAAGAGATCGTGTGAAAACAAAGCTGAAGTGGTTGCTCAGGACGAGAAGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtattatcattaactatggttgattttatgctgaactaatgtcaataaacattataatgcactccatgtttagtactcgtatgatttgctgggctg...

Basic information

species Oryza sativa
transcript LOC_Os09g36800.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G051129_T01 (Zea mays), 5'ss of exon 4
TATTAAGAGATCGTGTGAAAACAAAGCTGAAGTGGTTGCTCAGGACGAGAAGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtattatcattaactatggttgattttatgctgaactaatgtcaataaacattataatgcactccatg--------tttagtactcgtatgatttgctgggctg--------------------------------------------------------
||| |||||||| ||||||||||||||||||||||| || || || |||||||||||||| || ||||||||||| || || || || ||||||||||||||| || |||||||    | | |   |||||||||   | |||| |  |   |||||   | |   |   ||        |  |  ||   ||| |     |  ||                                                          
TATCAAGAGATCATGTGAAAACAAAGCTGAAGTGGTGGCACAAGATGAGAAGGAAAGTGGCCTTCGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatg---tttag--aattttatgcctgattaatttttactgacattgacaagttttgggtggaacaacctcaaccacctttatcacaattttagcgaccttatgttattgtaacacaccaaccatatactgatcctcactgtcaatttgtcag

upper sequence: LOC_Os09g36800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
TATTAAGAGATCGTGTGAAAACAAAGCTGAAGTGGTTGCTCAGGACGAGAAGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtattatcat-------taactatggttgattttatgctgaactaatgtcaataaacatt-------ataatgcactccatgtttagtactcgtatgatttgctgggctg--------------------------------------------------------------
||| |||||||| ||||||||||||||||| ||||| || || || |||||||||||||| || ||||||||||| || || || || ||||||||||||||| || |||||||       |   ||||  |||||  ||  |  |||    |  ||||   |        | ||      |||  ||||  ||    | |||||    |  |                                                               
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttatgtctgatt--attttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacat-caggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
















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|88584443|gb|CI701994.1|CI701994
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|58586315|gb|CF984623.1|CF984623
EST:     AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGCTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88429289|gb|CI690188.1|CI690188
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88448544|gb|CI693932.1|CI693932
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88903765|gb|CI711467.1|CI711467
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|38483247|gb|CF967049.1|CF967049
EST:     AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGCTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88591454|gb|CI707490.1|CI707490
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88585740|gb|CI701477.1|CI701477
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88306817|gb|CI671980.1|CI671980
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88581192|gb|CI698166.1|CI698166
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|25798307|gb|CA754268.1|CA754268
EST:     AGGANAGTGGTCTCCGAGCAACACTTAATCTCGGNCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCCTGGGGAGGCTGTT
genomic: AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|88587435|gb|CI705181.1|CI705181
EST:     GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: GGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|218479549|gb|FG949471.1|FG949471
EST:     AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATACAAACAGGAACTGGCTATGGAGCATGGCTCCATGGGGAGGCTGTT
genomic: AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTT
EST: gi|218496360|gb|FG958514.1|FG958514
EST:     AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCAT                         GCTATAGAAACAGGAACTGGCTATGGAGCATGGCTCCAT
genomic: AGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCAT

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: 64 (upstream exon), 71 (downstream exon)
Score: 39

TATTAAGAGATCGTGTGAAAACAAAGCTGAAGTGGTTGCTCAGGACGAGAAGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtatta ... caattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTTGCAGCTGGAACA




<











<


<