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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaccatccaatttctgcccatgtgcataggttatcctgatcttttggtcattttgcctgacctgtccttgttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC

Basic information

species Oryza sativa
transcript LOC_Os04g53190.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G000052_T01 (Zea mays), 3'ss of exon 7
gtttgtacca-tccaatttctgcccatgtgcataggttatcctgatc-ttttggtcattttgcctgacctgtc--cttgttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC
||||| || | ||  ||||||||| | ||||   ||| | |   | | ||   ||||||||  |||  || ||  | ||||||  ||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| || || || ||  |||| || || ||||||||||| 
gtttgaactaatctgatttctgccta-gtgcgctggtcagcgcaaacgttccagtcattttaactgtgctttctacgtgttcaatacagGCAAGAAGGGATTGCTCATGAGGTTCTTCAGTGGTATTTGTGCCGTATGGAGGGTTGGTTTGCCACCGACGCTGATTCAATTTCACTACAGGGTTGGGAT

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 7
gtttgtacca-tccaatttctgcccatgtgcataggttatcctgatctt-ttggtcattttgcc--tgacctgtccttgt--tcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC
|||||||| | || | || |||||  ||| ||  | | | |   | | |    ||||||||  |  ||   | ||| |||  |||| ||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||| || ||  |||| || || ||||| ||||| 
gtttgtactaatctacttcctgcctttgttcactgttcaacacaaacataccagtcattttaacagtgggttttccatgtgttcactacagGCAAGAAGGGATTGCTCATGAAGTTCTTCAGTGGTATTTGTGCCGTATGGAGGGTTGGTTTGCCACTGACGCAGATTCAATTTCACTACAGGGCTGGGAT

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA14G03610.2 (Glycine max), 3'ss of exon 6
------gtttgtaccatccaatt-tctgcccatgtgcataggttatcctgatcttttggtcattt-tgcctgacctgtccttgttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC
       || | |  |   |||  | ||  ||     || | || || |     |   || || | |   | | || ||  ||||     ||||   |||||| || | ||  | || || ||||||||||| ||| | |||||||||||||||||||| ||||| ||  | || || ||  |  ||||||| 
gtgattattggcataaaataatcctttgatcaccattattgattttcttagagctgaagtaatgtataatttaactttctctgttggatgcagGTTGGAAGGGCTTTCCCACAAGGTGCTACAGTGGTATTTATGCAGAATGGAAGGTTGGTTTGCTACAGATGCTGATACCATATCACTGAAATGTTGGGAT

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G59050.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtac-catccaatttctgcccatgtgcataggttatc-ctgatc---ttttggtcattttgcctgacctgtcct-tgttcaca-acagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC
|| || |  |||    | ||  | |||     |   || |  || |||   ||||     | |||| ||     |    | |||||  | |||   || ||  |||| ||| |||| ||||||||||| ||||||||||||||||| ||||||||| ||||||| ||  | |||||     || ||||||| 
gtatggaaacatattgtctcaactcattccgttgatttgttacttatccgcttttatatttgttgcatgcttaattagattttcacttatagGTTGGAGGGACTTGCCCATAATGTGCTTCAGTGGTACTTGTGCCGCATGGAAGGATGGTTTGCTGCTGATGCTGAAACCATCTCGGCAAAGTGTTGGGAT

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S24_237V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------------gtttgtaccatc----caatttctgcccatg-----tgcataggttatcctgatcttt----tggtcattttgcctgacctgtccttgttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC
                                                                               ||||| |   ||    |  | ||||    ||     || ||  ||| |  |||  |||    |||||| ||||  ||||  ||  | |      |||||||||| ||||| ||     | ||||| |||||||||||||| ||||||||||| ||||||||  | || || |||   |||||  ||||  ||||||||
gttggcttcggttcttgctgcatgggcttttgtcaatctgatggtcaggccacggattatgcgggtttggagtccccttgtttgcatggtctttgcggtgtctgaaattggaagttgtatgagttgtt-tgacgtttgcagtggtcaatttgattgacaagtggt-gaatgttacagGCAAGAGGGGATGGCATTCAAAGTTCTGCAGTGGTATTTGTGTCGCATGGAAGGATGGTTTGCAGCCGACGCAGACAACATCTCCGTTCAAAGTTGGGAC

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|33795011|gb|CF323384.1|CF323384
EST:     TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
genomic: TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
EST: gi|58691687|gb|CK080374.1|CK080374
EST:     TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
genomic: TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
EST: gi|29612733|gb|CB617746.1|CB617746
EST:     TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
genomic: TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
EST: gi|58611141|gb|CK038853.1|CK038853
EST:     GAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTA-TGGTGGCCGCATGG
genomic: GAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGT-GCCGCATGG
EST: gi|58663716|gb|CK052402.1|CK052402
EST:     TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
genomic: TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
EST: gi|58588158|gb|CF986466.1|CF986466
EST:     AAGGCCATTGCAACTTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATGGCGTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGG
genomic: AAGGCCATTGCAA-TTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGC-TCATGATGTTCTTCAGTGGTATTTGTGCCGCATGG
EST: gi|33797085|gb|CF324408.1|CF324408
EST:     TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
genomic: TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
EST: gi|58683985|gb|CK072672.1|CK072672
EST:     TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAG                         GCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA
genomic: TCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGA

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: 73 (upstream exon), 75 (downstream exon)
Score: 41

ACTGGCAAACTGAGGGAAGAAACTAAGGAAGACATTTCTATTGCGAAGGCCATTGCAATTGTTATGGAGAGAAATCCACACTTGAGgtttgtacca ... ttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggttatcctgatcttttggtcattttgcctgacctgtccttgttcacaacagGCAAGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGAC
                             gcctgac  putative branch site (score: 41)
                                       tccttgttc  putative PPT
             atctttt  TA-rich tract