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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG

Basic information

species Oryza sativa
transcript LOC_Os03g16980.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 8
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| | |    |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || |||
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatagattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG

upper sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 9
gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG
|||||||| | |||| |   || |   |  || ||| || || |||| | ||  ||| |  || | |  | ||| || ||  |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||| || || |||
gtaatgcttgttgaattc--tttagtttcttcccagcttctg-ccagatagttttggtggctaatatttt-catgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG

upper sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 5
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| | |    |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| ||||||                        
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatagattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGG------------------------

upper sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 15
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG---------------------------------
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| |      |  ||| || ||  | || ||| ||  || ||  ||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || ||                                  
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatatattggcggctaatctt--ttcacaatctt-tagCGGTCAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATAGTTTGTCTTCCACCGCGTTCTCAATTGGTTTGT

upper sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 10
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG---------------------------
||||||||  | ||||  | ||| |   ||||||   | |   | ||| |      |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || |||                           
gtaatgctttgttgaatgtatttta-ttttctcttgagctac-tgcagatatattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATGGTTTGTCTTCCACTGCATTCTCAATTG

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|33679182|gb|CF307421.1|CF307421
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|702654|gb|D48945.1|D48945
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|87024633|gb|CI259348.1|CI259348
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGCCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|14980762|gb|BI305440.1|BI305440
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|33675282|gb|CF303521.1|CF303521
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCATAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|325494210|gb|JG458734.1|JG458734
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|163926814|gb|EG715102.1|EG715102
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|87035546|gb|CI190168.1|CI190168
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29663852|gb|CB660127.1|CB660127
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|38478163|gb|CF962296.1|CF962296
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|33675428|gb|CF303667.1|CF303667
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|3766739|gb|AU030849.1|AU030849
EST:     CGTGTTGTTNGGAACTTCATTTGCTCAGGCCCNTACG                         TGGCGACCCCCTGACTNTTCAGAAGCCAGGAACNCAAACTAGGAGCTTCT
genomic: CGTGTTGTTAGTAACTTCA-TTGCTCAGG-CCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCT
EST: gi|58602898|gb|CK013426.1|CK013426
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|86823720|gb|CI258767.1|CI258767
EST:     GGGCGTGTTGTTAGTAACTTCATTGCTCAGCCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: GGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|58669067|gb|CK057753.1|CK057753
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29668687|gb|CB664962.1|CB664962
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29637730|gb|CB642739.1|CB642739
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|33680606|gb|CF308845.1|CF308845
EST:     ACATTGATGATGGGCNGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: ACATTGATGATGGGC-GTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29619074|gb|CB624086.1|CB624086
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|86477695|gb|CI120328.1|CI120328
EST:     CTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: CTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|86593436|gb|CI258465.1|CI258465
EST:     GTAACTTCATTGCTCAGNCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: GTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|86594978|gb|CI258232.1|CI258232
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGCCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|86250715|gb|CI007578.1|CI007578
EST:     ATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: ATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|29620631|gb|CB625642.1|CB625642
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
EST: gi|8858969|gb|AU096287.1|AU096287
EST:     TTAGTAACTTCATTGCTCAGGCCCGTACG                         TGGCGAGCCCCNTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTC
genomic: TTAGTAACTTCATTGCTCAGG-CCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCC-TGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTC
EST: gi|3763827|gb|AU030579.1|AU030579
EST:     AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG                         TGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG
genomic: AACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACGgtaatgctcg ... aattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG
                               ttattttcatacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT