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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccgccatttcatcttgatctctatttctgacccattgatttcttccattgaagctcacacgttttgtatgacttccctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGACTGAAGCCCAAGCCCAAGGCTGCGTAACTGAAGCATGCAGTTGCCATCTT

Basic information

species Oryza sativa
transcript LOC_Os08g25624.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 8
gtaagtccgccatttcatcttgatctctatttctgacccattgatttcttccattgaagctcacacgttttgtatgacttccctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGACTGAAGCCCAAGCCCAAGGCTGCGTAACTGAAGCATGCAGTTGCCATCTT
|||||   |    || | ||   ||||| | | ||  | |||   | ||||  ||| | | |       |  | | |  |   | |  |||| ||||| || ||||||||||||||||||||||||||||| || ||| |||| ||||||||||| ||| | || ||| |   |  || | || |||||| 
gtaagcatgtttcttaacctgtttctctgtctttgttctatttcatccttctgttgtatcaccattacatgctttcatctgtgtgta-tagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGACTTAAGCCCAAGCCGAAGACGGCTTAAATAGGGATTGTATTTTCCATCTC
















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|88473501|gb|CI410772.1|CI410772
EST:     AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCG                         GCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAC
genomic: AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCGgtaagtccgc ... cctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAC
EST: gi|88516280|gb|CI443934.1|CI443934
EST:     AACATCGGTTTTGTTGTTCAGGACTCCTGTTTGTCCTATCAACTCCCTCG                         GCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAG
genomic: AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCGgtaagtccgc ... cctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGA-
EST: gi|88519340|gb|CI446994.1|CI446994
EST:     AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCG                         GCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAC
genomic: AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCGgtaagtccgc ... cctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAC
EST: gi|88491816|gb|CI429088.1|CI429088
EST:     AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCG                         GCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAC
genomic: AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCGgtaagtccgc ... cctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGAC
EST: gi|88292064|gb|CI532656.1|CI532656
EST:     AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCG                         GCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAAGTGAAGAGGG
genomic: AACATCGGTTTTGTTCTTCAGGACTCCTGTTTCTCCTATCAACTCCCTCGgtaagtccgc ... cctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGA-GA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccattgatttcttccattgaagctcacacgttttgtatgacttccctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGACTGAAGCCCAAGCCCAAGGCTGCGTAACTGAAGCATGCAGTTGCCATCTT
                     agctcac  putative branch site (score: 3)
                                         cttccctct  putative PPT
                               ttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccgccatttcatcttgatctctatttctgacccattgatttcttccattgaagctcacacgttttgtatgacttccctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGACTGAAGCCCAAGCCCAAGGCTGCGTAACTGAAGCATGCAGTTGCCATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC