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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC

Basic information

species Oryza sativa
transcript LOC_Os04g41100.6
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179097_T03 (Zea mays), 3'ss of exon 1
gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC
|||| | |||  ||  |  ||| |||| | ||  |  ||   ||  || || |  |  ||  |||  |   ||   ||  ||   ||   |||||||||||||||||||||||||||| ||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||  |||||||||| 
gtaattattg--tttgctttcttttttcggttcacgtgttgtcttgaatctgttattgtgt-tgttgatacatggccagctttttta---cagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGAAGCCCATTAAAACCTTAT

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179097_T07 (Zea mays), 3'ss of exon 1
gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC
|||| | |||  ||  |  ||| |||| | ||  |  ||   ||  || || |  |  ||  |||  |   ||   ||  ||   ||   |||||||||||||||||||||||||||| ||||||||||||                                                              
gtaattattg--tttgctttcttttttcggttcacgtgttgtcttgaatctgttattgtgt-tgttgatacatggccagctttttta---cagGGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTG--------------------------------------------------------------

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 1
gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC
|||| | |   |||      || ||| ||||  | |  ||  ||  || || |  |      |||  |  |||   ||| ||   ||   |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| |||||  |||||||||| 
gtaattatc--tttttttacctttttctgttcac-atataatcttgaatctgttttttatgttgttgatagatggccatcttttcta---cagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTAT

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|29667472|gb|CB663747.1|CB663747
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|58691737|gb|CK080424.1|CK080424
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|29640024|gb|CB645033.1|CB645033
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|58587583|gb|CF985891.1|CF985891
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|33678455|gb|CF306694.1|CF306694
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAC                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|163929543|gb|EG709310.1|EG709310
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|58686625|gb|CK075312.1|CK075312
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|58687429|gb|CK076116.1|CK076116
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|29622943|gb|CB627954.1|CB627954
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTT
EST: gi|58669045|gb|CK057731.1|CK057731
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAACAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
EST: gi|58688555|gb|CK077242.1|CK077242
EST:     CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAG                         GGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT
genomic: CAGCTGTTGGAGGGTGTGAAGTATCTTCATGATAATTGGGTACTTCATAGgtaactgttg ... catataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC
                            tactgat  putative branch site (score: 2)
                                      cattttcc  putative PPT
                                       atttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgttgatttgacgctctatttttgtttgccaagtatcctcaaacctatcctgatgcctgtatactgatatgcattttccatataccagGGATCTGAAGACCTCAAATCTTTTGCTGAATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG