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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaatacatccttttgttgttccacaacaaactgtcatggacatcctttttttaattgatactattgtgttctag

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 47
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 47
lower sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 30
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaatacatccttttgttgttccacaacaaactgtc-atggacatcctttttttaattgata-ctattgtgttctag---------
 |||||||| || || ||||| || ||||||||||| |||||||||||||||||||||||||||||||| ||| | |||||||||||||||||||| |||||| || |   | | ||  | ||| ||  ||||||  ||  |    | | | ||||||||  ||| || | |   |  |   |         
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTTAATCTCCAGgtagaacatgcaaaaccact-gttatta-acaacattcttcctgcagcctttctttttttctttggtaaccaacattgttcggtcgttgtag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 47
lower sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 48
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaatacatccttttgttgttccacaacaaactgtcatggacatcctttttttaattgatactattgtgtt-ctag-------------------------------------------------------------
 |||||||| || || ||||| || |||||||||||||||||||||||||||||||||||||||||||| ||| | |||||||||||||| ||||| |||||| ||     | | ||  | ||| |        | ||  |    | |      || || |    | | |         |||                                                             
GAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATAATTCTAGCATACATTGATCTCAATCTCCAGgtagaacttgcaaaaccact-gttctgttgttgtagacccttgcagccgctagattgttgacccttgcaaaaccaccattagcaacaagattcttcgcaaagccttttttttcttggtaaccaacattgttcggttgttgtag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 47
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 50
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaa---aaatacatccttttgttgttccacaacaaactgtcatggacatcctttttttaattgatactattgtgttctag
 |||||||||||| ||||||| || ||||| ||||||||||||||||| |||||| ||||||| || |||||  | || |||||||| ||||||||| ||||| |||   ||| | ||   ||| || ||     || |   | | |    || || | |||| ||   ||| |||| || |||
CAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTTCCTATCGATGCTAAACCTCAACCCATCATCCTTGCCTACATTGAACTTAATCTTGAGgtataaatagaaacaaattaatttatt-ttaaggtactagtagacttatttatactgtattta-ttctcacttttgtattttag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 47
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 49
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaa---aaatacatccttttgttgttccacaacaaactgtcatggacatcctttttttaattgatactattgtgttctag
 |||||||||||| ||||||| || ||||| ||||||||||||||||| |||||| ||||||| || |||||  | || |||||||| ||||||||| ||||| | |   ||| | ||   ||| || |        |    | | |    || |  | |||| ||   ||| |||| || |||
CAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTTCCTATCGATGCTAAACCTCAACCCATCATCCTTGCCTACATTGAACTTAATCTTGAGgtatacattgaaacagattaatttattttaaggtggtag-tagacttatttatacggtattta-ttctcacttttgtattttag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 47
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 19
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaa--aaatacatccttttgtt---gttccacaacaaactgtcatggacatcc--tttttttaattgatactattgtgttctag--------------------------
 |||||||| || || ||||| || ||||||||||| ||||||||||||||    ||||| |||||||| ||  | || || ||||| |||||||||||||||  ||   | | ||    |||  |    | ||      |    |  ||||||||   || ||||  ||  | || |  | || |                            
TAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTTCCTATAGACATGGAACCCCAGCCAATTATCCTTGCCTATATTGACCTTAATCTTCAGgtattaattgagttcaagtatttacttaaatacctgttttattctttctggacatcaaattatttttctttcttctttatttttttcctttttttctttctccaaaccttacag

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|58658439|gb|CK047119.1|CK047119
EST:     ATGCTGAACCTCAGCCAATCATTNTGGCATACATGGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     ATGCTGAACCTCAGCCAATCATTTNGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58600986|gb|CK011514.1|CK011514
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAAGT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58597274|gb|CK007802.1|CK007802
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     ATGCTGAACCTCAGCCAATCA-TTTGGCATACA-TGATCTT-ATCTTCAG                         ACCC-TGCGGCAGCTA-AATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|88344329|gb|CI655723.1|CI655723
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAANTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58667817|gb|CK056503.1|CK056503
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAG                         ACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT
genomic: ATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaa ... tgtgttctagACCCTTGCGGCAGCTAGAATGCTGACTCCATCTGGAACTATGGGCCAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTTCCTATAGATGCTGAACCTCAGCCAATCATTTTGGCATACATTGATCTTAATCTTCAGgtaaaaaaaatacatccttttgttgttccacaacaaactgtcatggacatcctttttttaattgatactattgtgttctag

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG