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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttctggccctccccataattgttttacattcctgaatagccaactcaccattaaaaatattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA

Basic information

species Oryza sativa
transcript LOC_Os06g07210.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 16
---------------gtatgtcttctggccctccccataattgttttac----attcctgaatagccaactcaccattaaaaata-ttgttcagGAAAAC-GGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA---
                | | || |   |  || |  ||  || |||| |     || ||    |  |  |||||||| || |  | |||  || | |     ||          | | ||| || ||||| || ||||||||||| || ||||| ||||| |||||||||||||| |||||| ||||||||||||   
gtattgcccctatttttctttccttcagttctgca-atgttttttttcctcaggttactagggacacggctcaccatgaacaccacttgcacacgcagGTTAGCGATGGAAAGCCCGCGGAGGAAGACGTAGACGCTAAAATGGCACAGATGGTCTGTTCTTTGAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT

upper sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 16
--------------------------------------------------gtatgtcttctggccctccccataattgttttacattcctgaatagccaactcaccattaaaaatattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA---
                                                    |  |      ||   | | || | | ||||    ||||||| ||  |    | ||| |   |   ||| |||   || |     ||| |  |||||||||   |||| |||||||||||||| |||||||| ||||| || ||||||||||| |||||| ||||||||||||   
gtatattttctttcctttagtcctagaatattttccctcaaaagttactaaaacataactcagcatgcacaatgaatctttt----tcctgaaaagttactaaaacatgactcaccatgtgcagATGAATGATGGAAAGCCCACAGAGGAAG---ACGTAGAAGCTAAAATGGCACAAATGGTCTGTTCTTTTAACAACCGGGAAGAGTGCCTGGCGTGTGGAAGCT
















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|89179901|gb|CI044180.1|CI044180
EST:     CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|88840916|gb|CI080370.1|CI080370
EST:     CAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|58668190|gb|CK056876.1|CK056876
EST:     CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|8527825|gb|AU092640.1|AU092640
EST:     CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|88478126|gb|CI415397.1|CI415397
EST:     CGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|88282097|gb|CI403493.1|CI403493
EST:     CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|88837503|gb|CI078863.1|CI078863
EST:     TGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: TGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
EST: gi|88231414|gb|CI231263.1|CI231263
EST:     CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA                         GAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT
genomic: CTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGAgtatgtcttc ... tattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataattgttttacattcctgaatagccaactcaccattaaaaatattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA
                             aactcac  putative branch site (score: 2)
                                     attaaaaatattgttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttctggccctccccataattgttttacattcctgaatagccaactcaccattaaaaatattgttcagGAAAACGGCACCAAGGCTGCAGAGGAAGAGGACGTGGAAGCTAAAATGGCTCAAATGGTTTGTTCCTTGAACAACCGGGAGGAGTGCTTGGCGTGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG