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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT

Basic information

species Oryza sativa
transcript LOC_Os05g37170.8
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G000842_T02 (Zea mays), 3'ss of exon 3
gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
     |  |  ||    |   ||| |   || || |||||   || ||||  |  | ||||  |||||||  || || |||             ||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||
-----aggctgcagagtcgg-acaccccactcctctcttccacctctgtc--cgatcttgccgcctcttggagagaaaaga-------------cctttaattccatttgtatgtatgcagCAGCTGGATACCTTGCAGCTAGGCCCCCCACACTGGAGATCTTCCCTTCATGGCCAATGAGTCATCTACAGCAGCCATACAGT

upper sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 3
gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
              ||  | ||  |     | ||       || | | |    | | || ||||  ||| |      | || |   | |||         |||    || | ||  |   |||||   ||   |  |||| || ||  |    ||||||||||| ||||||||||||||||||||    |  ||    |||      
--------------ctgtcataattgaaagtcctcatggtcttttattttggtaatctt-caactccttcaacttg-gtgatcctcttacag--------attttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA---

upper sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G09430.2 (Glycine max), 3'ss of exon 2
gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggccttta-attccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
                     | |    |  |  |  | ||     | |  | ||  |||     | || |  ||          |||   |  |  | | |||    || | ||  || ||||||   ||   |  |||  |||||  |   |||||||||||| ||||| ||||||||||||||    |  ||     ||      
------------------ttgaaaaggaggataaggttcctccaccttttcatatgattga----tgttcataaagcctttatttttggtgatcctctgagattttccttttgtgattgtagCAGCTTTAT---TCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA---

upper sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 3
gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggccttta-attccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
            ||       | |   | | ||   ||| |    |  |  |  ||  |  | ||| |                 |||   |  |  | | |||    || | ||  || ||||||   ||   |  |||  |||||  |   |||||||||||| ||||| ||||||||||||||    |  ||     ||      
------------aaaaggaggataaggttcctccaccttttcatatgattgatgttcataaagccttt-------------atttttggtgatcctctgagattttccttttgtgattgtagcagCTTTAT---TCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA---

upper sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaa--ttccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
                       |    | ||  || | || ||  | |  | |||||   ||  ||||| || |          ||| |     ||   |  ||    || | ||  |   |||||   ||   |  |||| |||||  |    || |||||||| ||||||||||||||||||||    |  ||  | ||| | |  
-----------------------aaggggattaggt-tcctctcccttttgatattttgaaaa--tcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAA-ACCCAAAGA--

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|33655991|gb|CF278605.1|CF278605
EST:     ACAGTCATGAACACTGGTTACATACATGTAACTAGGAGGCAGCATAAATG                         CAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGC
genomic: ACAGTCATGAACACTGGTTACATACATGTAACTAGGAGGCAGCATAAATGgtgtgatccc ... tatgcagcagCAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggaaaagagagcgattgacaaggcctttaattccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCCCACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
                           tttaatt  TA-rich tract