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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagcccttctcacttttcccctctcgctccatttcttatttatattactacatatatttacatgttctttgttatatttttagtttgacttaaattgg...

Basic information

species Oryza sativa
transcript LOC_Os09g04790.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g04790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G031028_T01 (Zea mays), 5'ss of exon 1
GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaag----cccttctcacttttcccctctcgctccatttcttatttatattactacatatatttacatgttctttgttatatttttagtttgacttaaattgg
| ||  | ||| | ||||||||||||||||||||| | ||||||||||||||||| || || |||||||| || ||||| ||||| |||||||||||||||||||    | | | |   |      ||||  ||   ||||||     |   ||  |     |     |||| | | |  |  |    ||   | | | ||   
GAGCCAAAGTGCTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCTCCTACGGAGGCGCTTACGCTCCTTAACGGGAAGTGGATCCTCGCgtaagaaaccgccttttgatcccggtctctttcttagtttcttcccccttcgacagctggagtggtactgttgtctctcgtggtc--ggtgaaattcatatg--

upper sequence: LOC_Os09g04790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G870446_T01 (Zea mays), 5'ss of exon 1
GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagcccttctcacttttcccctctcgctccatttcttatttatattactacatatatttacatgttctttgttatatttttagtttgacttaaattgg-
| ||  ||||| | ||||||||||||||||||||| | |||||||||||||||||||| ||||| ||||| || |||||||||||||||||||||||||||||||       |  ||   |||  || ||   || |    ||  |   ||  |  |||||   | |  |      |    ||  | |||  ||   ||  
GGGCCAAGGTGTTGGAGCTCATCACGCAGCTCGAGACGCGCAACCCCACGCCGGCGCCTACCGAAGCGCTGACGCTCCTCAACGGCAAGTGGATCCTCGCgtaagaaaccgcctgttgatcccggtctctttcttccccccttcaacagctgga-gtatttgtctctcgtgatcggtgaaattcatctgatgtatcctgaa

upper sequence: LOC_Os09g04790.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G04020.1 (Arabidopsis thaliana), 5'ss of exon 1
GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagcccttctcacttttcccctctc------gctccatttcttatttatattactacatatatttacatgttctttgttatatttttagtttgacttaaattgg
| || ||| |   |||||||||||| ||||||||| |    ||||| || || || || | ||| || ||    |||||||||||||| ||||||||||||||||  ||| |   | |    |||||       |  ||| |  ||||  | ||    || | ||| ||     |   || || | |    || | ||   |    
GAGCTGAGATCAGCGAGCTCATCACACAGCTCGAGTCTAAGAACCCTACTCCAGCTCCTAACGAAGCTCTGTTTCTCCTCAACGGCAAATGGATCCTCGCgtaagtacttttagttctgatactctcctaggcacggcatgtaatattagttttgtcccaaacatt-actcaaaccg-gtgatctctaagcttcgtctagga----

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|29682126|gb|CB678401.1|CB678401
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29670575|gb|CB666850.1|CB666850
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29669223|gb|CB665498.1|CB665498
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29669224|gb|CB665499.1|CB665499
EST:     CGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|58689543|gb|CK078230.1|CK078230
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         CTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|13420465|gb|AU174555.1|AU174555
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29613378|gb|CB618391.1|CB618391
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|58595824|gb|CK006352.1|CK006352
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29667091|gb|CB663366.1|CB663366
EST:     CGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29670576|gb|CB666851.1|CB666851
EST:     CTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29630117|gb|CB635126.1|CB635126
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|300216220|gb|HO088005.1|HO088005
EST:     CCGGCG-CCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29673852|gb|CB670127.1|CB670127
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|58610507|gb|CK038219.1|CK038219
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29617782|gb|CB622794.1|CB622794
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29667042|gb|CB663317.1|CB663317
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29627668|gb|CB632679.1|CB632679
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|58600409|gb|CK010937.1|CK010937
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGGC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29617781|gb|CB622793.1|CB622793
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
EST: gi|29682125|gb|CB678400.1|CB678400
EST:     CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGC                         GTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC
genomic: CCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCC

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), 75 (downstream exon)
Score: 58

GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagccctt ... gtgactacagGTACACCTCATTTTCACAGCTATTCCCACTATTGGGGTCTGGTAGTTTGCCTCAGCTTGTCAAGGTGGAAGAAATATCACAAACTATTGATTCTGAGAAC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCGGAGGTGGTCGAGCTCATCACGCAGCTCGAGGCCCGCAACCCCACGCCGGCGCCCACCGAGGCGCTCACCCTCCTCAACGGCAAGTGGATCCTCGCgtaagcccttctcacttttcccctctcgctccatttcttatttatattactacatatatttacatgttctttgttatatttttagtttgacttaaattgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc