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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACAGTGGTCGTGAGGATCAGATAGAGGGAGTTAGTGAATGCATTATCATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatgattagcttgcaccctttgattgtgctatagcatactatgatggcaaacttgtctttcctgagccactgtactacttacatcagacatggcgaaattacagcttcaccggcagtaacattgttagaacttctggatcaaccagacaaacctcacgttttactgataatacccttttttccttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g41490.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41490.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G178236_T01 (Zea mays), 5'ss of exon 7
CATACAGTGGTCGTGAGGATCAGATAGAGGGAGTTAGTGAATGCATTATCATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatgattagcttgcaccctttgattgtgctatagcatactatgatggcaaacttgtctttcctgagccact-gtactacttacatcagacatggcgaaattacagcttcaccggcagtaacattgttagaacttctggatcaaccagacaaacctcacgtt-ttactgataatac-ccttttttccttgcag
|||||||||||||| |||||||||||||||||||||||||||||||||||||||| || |||||||| || || || ||||||||||||||||| |||||||||| |  |||   ||  ||||||  | |||| ||  ||  |         || ||||   |   |||| |  ||  | |  |||     | |  | || |  ||     || ||  | | |      | | | || | ||  ||    | ||||||| || | | ||  ||||   |  || |||  | ||||||
CATACAGTGGTCGTCAGGATCAGATAGAGGGAGTTAGTGAATGCATTATCATGGGCATTCCCATGCAGCTCGGTACCGGTATTCTCAAAGTCAGGCAAAGgtacgtacaattttattatacccttaaactgtggtacggcgca--------acacactt---tgcactgaacttctcatccagcttgttgaaaagtttgccatcttttttttttacttgaaatttt-ccggtggtacctgtgtttc---taaacaaaccacatgatattgttgatttgatgccatttccctttgcag

upper sequence: LOC_Os04g41490.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv06s0004g03730.t01 (Vitis vinifera), 5'ss of exon 7
-CATACAGTGGTCGTGAGGATCAGATAGAGGGAGTTAGTGAATGCATTATCATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatgattagcttgcaccctttgattgtgctatagcatactatgatggcaaacttgtctttcctgagccactgtactacttacatcagacatggcgaaattacagcttcaccggcagtaacattgttagaacttctggatcaaccagacaaacctcacgttttactgataatacccttttttccttgcag
   || |||||| | || ||  |||| || ||||| ||||||||||| ||||||||||||||||||||||| |||||||| || || ||||| ||||| ||||| | |||  ||| |  ||   ||  |     | || |  | ||  ||| |      ||||  |    |   |   |  |  ||   ||          | ||                                                                                          
CTGTA-AGTGGTAGAGATGACAAGATTGAAGGAGTAAGTGAATGCATAATCATGGGTATACCCATGCAACTGGGCACTGGAATACTTAAAGTTAGACAGAGgtatgtatg-ctagatgacaa--ttcaagcactcaat-gttttcttggatagttttgatgtcaatttcaa--taacttgttgtttctctcgagtggttttatatgc----------------------------------------------------------------------------------------
















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|88231601|gb|CI231450.1|CI231450
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
EST: gi|88486928|gb|CI424199.1|CI424199
EST:     AGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: AGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
EST: gi|86539733|gb|CI179939.1|CI179939
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
EST: gi|88368598|gb|CI675145.1|CI675145
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTG
EST: gi|58691524|gb|CK080211.1|CK080211
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
EST: gi|88272960|gb|CI388416.1|CI388416
EST:     TATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTTATCCAAATATTGGCGT
genomic: TATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCC-AATATTGGCGT
EST: gi|218488711|gb|FG960953.1|FG960953
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
EST: gi|112785739|gb|EE591310.1|EE591310
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTTAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
EST: gi|396941602|gb|HO188259.1|HO188259
EST:     ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAG                         GCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG
genomic: ATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTG

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: 35 (upstream exon), 73 (downstream exon)
Score: 7

CATACAGTGGTCGTGAGGATCAGATAGAGGGAGTTAGTGAATGCATTATCATGGGTATACCCATGCAACTTGGCACTGGTATTCTCAAAGTCAGACAAAGgtacgaatga ... ttccttgcagGCTTGACCATTTGCCTGAATTTAAATATCAGCCTGATCCAATATTGGCGTGATACAAGCTAGAAGCCTAGAACCAGCTTAATTTGTCTGAAGCTGGAATT




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