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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattattgcacatacaacatctattctgatatttcttcgatgcaatttatagattatgcattaacactcagctgatgtgttcctttttcacttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGAGGGGCCTGGGCATGCCTGCACCCTGCCAGCGTGCCCTGAATGTGTAAAT

Basic information

species Oryza sativa
transcript LOC_Os09g39462.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G009575_T01 (Zea mays), 3'ss of exon 4
-----gtatt-attgcacatacaacatctattctgatatttcttcgatgcaatttatagattatgcattaacactcagctgatgtgttcctttttcacttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGAGGGGC-CTGGGCATGCCTGCACCCTGCCAGCGTGCCCTGAATGTGTAAAT
     | ||  |  |   ||  ||| || | |  | |    || | |||  ||  |    |||    |||   ||  ||| |    ||    ||| ||| || |||||||||||||||||| || | |||||||||||||| || |||||| | |||||||| | | ||||||||||||| |||||| ||||  ||||    | |  
atttggaatggagggggtatttaacttcgaatgagttgaaactcc-atgagatgcactagttaaat-ttagttcttggctaacagatt----ttttactggtacagACTCACCAACAACAATCTAATGCTAGTTTGCGCTTTGCTCGGCCCTGGTGAGGGGCGCCGTGCATGCCTGCACC-TGCCAGTGTGCAATGAACACATTACC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G103345_T01 (Zea mays), 3'ss of exon 3
gtattattgcacatacaacatctattctgatatttcttcgatgcaatttatagattatgca---ttaacactcagctgatgtgttcctttttcacttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGAGGGGCCTGGGCATGCCTGCACCCTGCCAGCGTGCCCTGAATGTGTAAAT-
 | || | |   |       |  | |  |||     |   |  |     |   | ||   |   ||    ||   || |    |   |||||   | || ||||||||||||||||||||||| |||||| | ||||| ||||||||||| ||||||||| ||||||||||||||| |||||| ||||    ||    | |   
atgttgtagtctaggagtttttaagttcgattgaattgaaactcttgaaacgaactagttaaatttgtttcttgtctaacagat---ttttttgttggtacagACTCACCAACAACAACCTGATGCTAGTCTACGCTTTGCCCGGCCCCGGTGAGGGGCCCGGGCATGCCTGCACC-TGCCAGTGTGCAACAAACACATTATCC

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0106g00640.t01 (Vitis vinifera), 3'ss of exon 3
gtattattgcacatacaacatctattctgatatttcttcgatgcaatttat-agattatgcattaacactcagctgatgtgttcctttttcac------ttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGAGGGGCCTGGGC-ATGCCTGCACCCTGCCAGCGTGCCCTGAATGTGTAAAT
   | | |  || | | ||||  |||  |  | || |||  | || ||  | |  |||      ||  |||   | ||| |||  ||| |  |      || ||||| |||| ||||| ||||||||  | |||||  | |||||||||||||| | |||||| ||||| |||||||||||||||||||     || ||  |  ||| 
---tgaatatactttctacata-atttggtcagtttttc--tccacttagttattttacatgccaaatctcgcttaatg-gttattttgttgcatgtctttatgcagTCTCATCAACAGCAACCTGATACAAGTTTTGGATTAGCCCGGCCCCGGTAAGGGGCATGGGCCATGCCTGCACCCTGCCAGCTGAAACTCAAGCTTGAAA-

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|163926013|gb|EG712317.1|EG712317
EST:     CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
genomic: CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
EST: gi|44664744|gb|CR278178.1|CR278178
EST:     ATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCTGATGA
genomic: ATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
EST: gi|58599912|gb|CK010440.1|CK010440
EST:     CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
genomic: CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
EST: gi|58609649|gb|CK037682.1|CK037682
EST:     CAGTAGTCACATATGTACATCCACAGGAACCCATGGGTGCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
genomic: CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
EST: gi|58660413|gb|CK049093.1|CK049093
EST:     CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
genomic: CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
EST: gi|66924759|gb|CX111607.1|CX111607
EST:     CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
genomic: CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
EST: gi|218479471|gb|FG952619.1|FG952619
EST:     CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAG                         ACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA
genomic: CAGGAGTCACATATGTACATCCACAGGAACCCATGCGTCCATTTGCACAGgtttgtatcc ... acttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatagattatgcattaacactcagctgatgtgttcctttttcacttgtgcagACTCACCAACAACAACCTGAAGCTAGTTTGCGCTTAGCCCGGCCCCGATGAGGGGCCTGGGCATGCCTGCACCCTGCCAGCGTGCCCTGAATGTGTAAAT
                                 tgttcctttttcactt  CT-rich tract
     tagattat  TA-rich tract