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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttgtgtgtattcttcactaatgtagacttgtgaagtgttacatgataatatccctcgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACATGGGGCTGGTCCAGGCACGAATTGTGGAAGTCCAGATGTGGTTGCTGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g42850.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42850.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 10
-------------------------gtaattcttg-tgtgta-ttcttcacta-atgtagacttgtgaagtgttacatgata-atatccctcgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACATGGGGCTGGTCCAGGCACGAATTGTGGAAGTCCAGATGTGGTTGCTGCTG---
                          | | ||||  | | || || |||| |   | |||   |   |  |  || ||||||  |    || |||| |||||||||||||| ||||  ||||||| |||||||||||||||||||||||||||| ||||| ||||| || |   ||||  || ||||||  ||  || ||    
accacacatatgttagttacaaaaaattactcttaatatctactttttcattgtgtatagcacttctagttacta-atgatatgttatacttgcactgcagATTGCTATTAGTGCATTATTAGGACATGACAGTTACCTTGTCATGCGACATGGTGCTGGACCAGGAACAA---GTGGGGGTACAGATGAAGTGACTACTCAGA

upper sequence: LOC_Os01g42850.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 16
gtaattcttgtgtgtattcttcactaatgtagacttgtgaa-gtgttacatgataatatccctc-gcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACATGGGGCTGGTCCAGGCACGAATTGTGGAAGTCCAGATGTGGTTGCTGCTG
|| |  | | |  | || ||| | |||||||||| |  ||| |||||||||| ||||  ||||| |||| |||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||  |  |||| |  | |   ||||||  ||||  
gtgaaccctctaggcatccttgaataatgtagaccttggaatgtgttacatgctaatgcccctctgcactgcagATTGCTATCACTGCAGCATTAGGGTATGATAGTTACCTTGTCATGCGACATGGGGCTGGCCCTGGCATAAGCTGTGAAGCTTCCAGTGTGGTCACTGCCA
















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|29677767|gb|CB674042.1|CB674042
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29672225|gb|CB668500.1|CB668500
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29667791|gb|CB664066.1|CB664066
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29641126|gb|CB646133.1|CB646133
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|33682080|gb|CF310319.1|CF310319
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAN
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACA-
EST: gi|29674598|gb|CB670873.1|CB670873
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29640245|gb|CB645254.1|CB645254
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29627979|gb|CB632990.1|CB632990
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAATAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29629460|gb|CB634469.1|CB634469
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAATAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29674600|gb|CB670875.1|CB670875
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
EST: gi|29642677|gb|CB647684.1|CB647684
EST:     CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAG                         ATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT
genomic: CAAGGGAAAGTAGGTGGCTTCCAACACTTCTCTGCGCAAATGAAAACAAGgtaattcttg ... cgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcactaatgtagacttgtgaagtgttacatgataatatccctcgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACATGGGGCTGGTCCAGGCACGAATTGTGGAAGTCCAGATGTGGTTGCTGCTG
    cactaat  putative branch site (score: 2)
                                      tatccctc  putative PPT
                           ttacatgataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcttgtgtgtattcttcactaatgtagacttgtgaagtgttacatgataatatccctcgcaccgcagATTGCTATTACTGCAGCATTAGGATATGACAGTTACCTTGTCATGCGACATGGGGCTGGTCCAGGCACGAATTGTGGAAGTCCAGATGTGGTTGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT