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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgaaaaatcccgaattcccctatgctctgcttagttgtcatcttgcttttagaatatttgctttacacataactagcataacatcctttctttcacatcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA

Basic information

species Oryza sativa
transcript LOC_Os09g24200.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24200.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G061620_T01 (Zea mays), 3'ss of exon 10
--gtgagtcgaaaaatcccgaattcccctatgctctgcttagttgtcatcttgcttttagaatatttgctttacacataactagcataacatcctttctttcac-atcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA
  || |||| |   ||   |      |  |||      |||   ||  |  ||| | |  | |        |    |||   |   || |  |||    |||   || |  |||||||||  |||||||||||||| || || || ||||| ||||||||||| ||||||||| ||||||||||||| || ||||| ||| | ||||||||| 
gtgtaagtcaatggattatggg----caaatgg---atttaagagtggttctgcgtgtcaacttccataggtttttatattcaatttacccccctcaaattcttgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCCTGCAACAAGAACGAGCAGCTGGCCGCCAACTACCTCTTGGATCACATGC

upper sequence: LOC_Os09g24200.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G061620_T02 (Zea mays), 3'ss of exon 10
gtgagtcgaaaaatcccgaattcccctatgctctgcttagttgtcatcttgcttttagaatatttgctttacacataactagcataacatcctttctttcac-atcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA
|| |||| |   ||   |      |  |||      |||   ||  |  ||| | |  | |        |    |||   |   || |  |||    |||   || |  |||||||||  |||||||||||||| || || || ||||| ||||||||||| ||||||||| ||||||||||||| || ||||| ||| | ||||||||| 
gtaagtcaatggattatggg----caaatgg---atttaagagtggttctgcgtgtcaacttccataggtttttatattcaatttacccccctcaaattcttgatgcgcagCTTGAAGGGATGGGCTTTGACCGGGCACTCGTCCTGGAAGTGTTCTTCGCCTGCAACAAGAACGAGCAGCTGGCCGCCAACTACCTCTTGGATCACATGC

upper sequence: LOC_Os09g24200.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G105772_T01 (Zea mays), 3'ss of exon 10
gtgagtcgaaaaatcccgaattcccctatgctctgcttagttgtcatcttgcttttagaatatttgcttt-acacataactagcataacatcctttctttcacatcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA
||  |||||   |||  || |    | || | |  |||     | |      | |||  |  || | ||| | |   || |  |||  ||||   || ||||    |  |||||||||  |||||||||||||| || || || ||||| ||||||||||| ||||||||| | ||||||||| | || ||||| ||| | ||||||||| 
gtatgtcgatggatcttgactagttc-atacac-acttgcccttaactgcattcttaccaccttggtttttatatccaatt--catcccatcacatccttcatgcgc--agCTTGAAGGGATGGGCTTTGACCGGGCACTGGTCCTGGAAGTGTTCTTCGCGTGCAACAAGAATGAGCAGCTGACCGCCAACTACCTCTTGGATCACATGC

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|27554427|gb|CA998327.1|CA998327
EST:     TGCCACAGACCATAGCAGTTACTCCAGAGGAGAATGAAGCCATACTTCGT                         CTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCT
genomic: TGCCACAGACCATAGCAGTTACTCCAGAGGAGAATGAAGCCATACTTCGTgtgagtcgaa ... acatcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCT
EST: gi|218493918|gb|FG945281.1|FG945281
EST:     TGCCACAGACCATAGCAGTTACTCCAGAGGAGAATGAAGCCATACTTCGT                         CTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCT
genomic: TGCCACAGACCATAGCAGTTACTCCAGAGGAGAATGAAGCCATACTTCGTgtgagtcgaa ... acatcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatatttgctttacacataactagcataacatcctttctttcacatcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA
                          gcataac  putative branch site (score: 3)
                                  tcctttctttcacatc  CT-rich tract
                   ataacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgaaaaatcccgaattcccctatgctctgcttagttgtcatcttgcttttagaatatttgctttacacataactagcataacatcctttctttcacatcctaagCTTGAAGCAATGGGCTTTGACCGCGCGCTTGTTCTGGACGTGTTCTTCGCTTGCAACAAGGACGAGCAGCTGGCGGCAAACTATCTCCTAGATCACATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA