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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttacttcctgctgccttccccttgcacatgttgcgtgcatgtttacatgtaatcctaacagtattcgtttcttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGTTGAGCCGTGAGAGCTTCACTCATGTTATGGACAGAA

Basic information

species Oryza sativa
transcript LOC_Os03g12710.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 6
gttcttacttcctgctgccttcccc-ttgcacatgttgcgtgcatgtttacatgtaatcctaa---cagtattcgtttcttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGTTGAGCCGTGAGA-GCTTCACTCATGTTATGGACAGAA
     | || || ||||||||| ||  | || || |||  ||||   |||    | || ||||   || | | | || |||||| ||||||||||||||| || | |||||||||| ||||||| ||||||||| |||||||||| | |||||||||    |   | |||    |   | || |||   
----gttctccccgctgccttctccgctccatatattgtctgcactattatgcctcatgctaatatcaatgtccattacttgacacagGCTGGAGAAACAATCGAGCACAACCAGCTTCATACCCAAGTCGATTACAGAGCGTTTTACCCGTTGAGCTTCCACTCGTTTCCAGAACAATGTG-ACATTT
















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|218497339|gb|FG955291.1|FG955291
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|58597240|gb|CK007768.1|CK007768
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|25803337|gb|CA759298.1|CA759298
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|88374455|gb|CI515939.1|CI515939
EST:     ATTGAAACAANTTCAGAGCAAATAATGAGATCTTTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|88460250|gb|CI529325.1|CI529325
EST:     TGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: TGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|25803336|gb|CA759297.1|CA759297
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|2427208|gb|C71671.1|C71671
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|58679347|gb|CK068034.1|CK068034
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
EST: gi|88996329|gb|CI389040.1|CI389040
EST:     ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAG                         GCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA
genomic: ATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGA

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: 66 (upstream exon), 72 (downstream exon)
Score: 20

CTGCATACAATTTTAGATGAAATGATACTTGGGGGACAAGTGATTGAAACAAGTTCAGAGCAAATAATGAGATCTGTCGAAGAGATTGCAAGgttcttactt ... cttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGTTGAGCCGTGAGAGCTTCACTCATGTTATGGACAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgttgcgtgcatgtttacatgtaatcctaacagtattcgtttcttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGTTGAGCCGTGAGAGCTTCACTCATGTTATGGACAGAA
                                      ttcgtttctt  CT-rich tract
             atgttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttacttcctgctgccttccccttgcacatgttgcgtgcatgtttacatgtaatcctaacagtattcgtttcttgacgcagGCTGGAGAAACAGTCAAACACAACCAGCCTCATACCGAAGTCGATTTCAGAGCGTTTCAGCCGTTGAGCCGTGAGAGCTTCACTCATGTTATGGACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT