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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatttgttccactagtcaaagcagtttatgtgttgtttcttcacccttccttcgtactcaatttcttaccatgattgctgcttttggaatgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCAGCCAGCCGCCTGTTGTCTTTAAGACCCAGCTATACACTCTGACTGGTGT

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 2
---gtatttgttccactagtcaaagcagtttatg-tgttgtttcttcacccttccttcgtactcaatttct-taccatgattgctgcttttggaatgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCAGCCAGCCGCCTGTTGTCTTTAAGACCCAGCTATACACTCTGACTGGTGT
   | ||||| |    | | |       || ||  | ||  |||         |   | || |   |||   ||| || | |  || |||| ||||| | |||||||| |||||||||||||||||||  ||| |||||||||||||| ||||| |||||||| ||  |||| || ||||  ||||||||||| || ||||||||
ccagaatttggtattatggcc----tgcttcataatattagttccatgttgcgcagacatatttttttttcatactataacta-tgttttttgaatgatctccagTAAACGTGAAATGGCAGAAGGAGGTCTTTCCAGGCATAGAGATTGACACTAGCCAGCCTCCGATTGTTTTGAAGAGTCAGCTATACACACTAACTGGTGT

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G017086_T05 (Zea mays), 3'ss of exon 1
-gtatttgttccactagtcaaagcagt-ttatgtgttgtttcttcacccttccttcgtactcaatttcttaccatgattgctgcttttggaatgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCAGCCAGCCGCCTGTTGTCTTTAAGACCCAGCTATACACTCTGACTGGTGT
   || || | |  |  | | | |||  || |||||| | || | |   |   | | |       | |  ||     ||  || || | ||||| ||||||||||||||||||||||||||||||  ||| |||||||||||||| ||||| |||||||| ||  |||| || ||||| ||| | ||||| || ||||||||
gagatatgcttctgttttaacaccagaattttgtgttatgtcataatattagttccatgtgtg--tacagacatattttaatgtttattgaatgatttccagTAAGCGTGAAATGGCAGAAGGAGCTCTTTCCAGGCATAGAGATTGACACTAGCCAGCCTCCGATTGTTTTCAAGACTCAGTTGTACACACTAACTGGTGT
















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|88364309|gb|CI612258.1|CI612258
EST:     TCCGCCGCCTCCTCCGCCGGCGCGCCGCCGATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: TCCGCCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|29646291|gb|CB651298.1|CB651298
EST:     ATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: ATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|29689095|gb|CB685370.1|CB685370
EST:     ATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: ATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|88315540|gb|CI615412.1|CI615412
EST:     TCCGCCGCCTCCTCCGCCGGCGCGCCGCCGATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: TCCGCCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|58681280|gb|CK069967.1|CK069967
EST:     ATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: ATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|33795963|gb|CF323849.1|CF323849
EST:     ATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: ATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|88726053|gb|CI749708.1|CI749708
EST:     TCCGCCGCCTCCTCCGCCGNCGCGCCGCCGATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: TCCGCCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|29679500|gb|CB675775.1|CB675775
EST:     ATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: ATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|29615418|gb|CB620430.1|CB620430
EST:     GCAGCCATGCCGACCG                         TAAGCGTGAAATGGCACAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: GCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|29674105|gb|CB670380.1|CB670380
EST:     ATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: ATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|88351105|gb|CI623327.1|CI623327
EST:     TCCACCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: TCCGCCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|88357489|gb|CI623543.1|CI623543
EST:     TCCACCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGACATGCCGACCG                         TAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: TCCGCCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
EST: gi|29615343|gb|CB620355.1|CB620355
EST:     GCAGCCATGCCGACCG                         TAAGCGTGAAATGGCCCAAGGAGACCTTCCCAGGCATAGAGATAGACACCA
genomic: GCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 68 (upstream exon), 72 (downstream exon)
Score: 47

TACCTCCGTCGCCGTCCGGTTCCTTTCTCTTCCTCCAAGTAAACTCGGTCTCCGCCGCCTCCTCCGCCGCCGCGCCGCCGATTCGCAGCCATGCCGACCGgtgagctccc ... tgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCAGCCAGCCGCCTGTTGTCTTTAAGACCCAGCTATACACTCTGACTGGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccttcgtactcaatttcttaccatgattgctgcttttggaatgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCAGCCAGCCGCCTGTTGTCTTTAAGACCCAGCTATACACTCTGACTGGTGT
                  ttcttac  putative branch site (score: 47)
                                             tgctttcc  putative PPT
               aatttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgttccactagtcaaagcagtttatgtgttgtttcttcacccttccttcgtactcaatttcttaccatgattgctgcttttggaatgctttccagTAAGCGTGAAATGGCAGAAGGAGACCTTCCCAGGCATAGAGATAGACACCAGCCAGCCGCCTGTTGTCTTTAAGACCCAGCTATACACTCTGACTGGTGT

- - - - - - - - - - - - - - -tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct