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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g58040.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 8
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG
            |  ||    | ||  | ||| |  || || ||       || |   ||| |||||    || | | ||    |||| ||  ||||||||||| ||||||||||| ||||| || || ||||| || || ||||| ||||| |||||||||||||||||||||||||| || 
------------gcaagcccgtagctca-aaacaaaccgactgcttt---ctgcaatgttt-tctgatcccctctgtatcccg-ttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 9
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG
         |  |     |  | | |    |     |  | |  || ||||   ||        || |||||  |  || |    | ||  |||||||||| || |||||||| ||| ||||||||||||||||    || ||||| || || ||||| || || || || ||||||||||||
--------gttagtgcaaactttgaaatttagagttctgaaaaaaaaaaaaaaaac--------tgcaatgccataactgttgtattctcttgcagATCCTATCAAAGAAAGGTGTTGTCATTCTTCCAGACATATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 7
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG
                                         |     |||||  |  | || |||  | ||  ||     ||  ||   |   |||||  |  | ||||| ||| |  |  | || || |||||||| || ||||| || ||||||||||||||||||||||| ||||| |||
---------------------------------------gtataggaaaaatcaaaaagttttctagattgaattg---atggtttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 7
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgc-agATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG
                                         |  |  |||||  |    || |||| | ||     ||| ||  ||  |    | ||||  |  | ||||||||| |  |  |  | ||||||||| | || ||||| || ||||||||||||||||||||||| ||||| |||
---------------------------------------gtatgagaaaaataaaaagctt-tctggattgaa---tctatggttttttgtgactagATTTTTGCGAAGAAAGGCATCATTGTGTTGCCAGACATCTTGGCAAACTCAGGAGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 7
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG
                                         |     |||||  |  | || |||  | ||  ||     ||  ||   |   |||||  |  | ||||| ||| |  |  | || || |||||||| || ||||| || ||||||||||||||||||||||| ||||| |||
---------------------------------------gtataggaaaaatcaaaaagttttctagattgaattg---atggtttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

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|86600065|gb|CI258405.1|CI258405
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|58680379|gb|CK069066.1|CK069066
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|163920099|gb|EG712029.1|EG712029
EST:     GCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: GCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|286451|gb|D15259.1|D15259
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|86823598|gb|CI258678.1|CI258678
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|29674432|gb|CB670707.1|CB670707
EST:     AGTACATCATTGAGGCTGCAACCCTCCCCACAGCCCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTATCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|86594959|gb|CI258213.1|CI258213
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|8527504|gb|AU092319.1|AU092319
EST:     AGTACATCATTGAGNCTGNAAACCACCCCACAGACCNTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|58593842|gb|CF992150.1|CF992150
EST:     AGTACATCATTGAGGCTGCAAGCCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|3760756|gb|C98010.1|C98010
EST:     GTACATCATTGA-GCTTGCAAACCACCCAACAGA-CCTGAGGCAGATGA-                         ATCCTGTCCAAGAAA-GCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: GTACATCATTGAGGC-TGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|86594966|gb|CI258220.1|CI258220
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
EST: gi|29679311|gb|CB675586.1|CB675586
EST:     AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAG                         ATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC
genomic: AGTACATCATTGAGGCTGCAAACCACCCCACAGACCCTGAGGCAGATGAGgcaagcacat ... ccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG
                              ctttctctctgaattc  CT-rich tract
      aaaatgta  TA-rich tract