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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagataatttctttgatgtttttttggctttccataacctgtactcctgtattaacaaaatatagtgtatgtttaatttttttgctttgttgattcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT

Basic information

species Oryza sativa
transcript LOC_Os07g24190.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 9
gtaaaagataatttctttgatgtttttttggctttccataacctgtactcctgtattaacaaaatatagtgtatgtttaatttttttgctttgttgat-tcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT
        |||||  |   |  | |||    | ||   |   ||||  ||    |   |    ||| | |   | |||||||  |||  ||||||  | |||||||||||||| |||||||||||||| |||||||||||  || | ||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||
-------gtaattgtt---acatctttgaatcatttgtttgtctgtcttctataacctatgggatacaataggtttttaattacttttgtttgtttgtatcacagGTCCGAGTCTCTGCTGTACTAACAAATGCTCCATATTTGTTAAACTTGGATTGTGATCACTACATCAACAACAGCAAGGCTATAAAGGAAGCAATGTGTT

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 9
gtaaaagataatttctttgatgtttttttggctttccataacctgtactcctgtattaacaaaatatagtgtatgtttaatttttttgctttgttgattcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT
           |   | ||   | |||    | ||   |    |||  ||        |     || | ||| | ||   |  || || ||   ||  |||||||||||||| |||||||||||| | |||||||| ||  || | ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||||||||
----------gtaattatggcatctttgaatcatttgtttgtatgtcttctatagcctatgtggtacaatgtgttttatttacttctgtttgtctgtatcacagGTCCGAGTCTCTGCTGTACTATCAAATGCTCCTTATTTGTTAAACTTGGATTGTGATCACTACATCAACAACAGCAAAGCTATAAAGGAAGCAATGTGTT

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaagataatttctttgatgtttttttggctttccataacctgtactcctgtattaacaaa----atatagtgtatgtttaatttttttgctttgttgattca-cagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT
      |  ||| |   | | |        |  |||| ||   | |  | | || |  | |||    |||   | ||  ||||  ||  |||  |||   ||  |  |||||||||| |||||||| || || ||||| |||||  || | ||||||||||||||||| |||||||| || || |||||| | | |||  | |||||||
------gtaaatattagtaaagcgacaactgaattccgtatgttcttatgcagtctacaaaaatcttataatttttacctttatcttcattggcttgcccatcaaatagGTCCGAGTCTCTGCTGTGCTCACAAATGCACCATATCTGTTGAACTTGGATTGTGATCACTACATCAATAACAGTAAGGCTCTTAGGGAGTCTATGTGTT

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaagataatttctttgatgtttttttggctttccataacctgtactcctgtattaacaaaatatagtgtatgtttaatttttttgc---tttgttgattca--cagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT
                   ||||   || |      || | |   |     |||  | | |||  || || |   ||| ||||  | |     || ||  || |  ||||||||||| |||||||| || || ||||| || ||  |  | || |||||||||||||| ||| ||||||| ||||||||| | ||||| ||||||||||
-----------------gtatgtagcttggtaaaatcacatctattctaggtgtcctgataaag-at-gtctgaattttatttcctggtgggcttattctttaaaacagGTCCGAGTCTCTGCTGTTCTTACGAATGCACCTTATCTATTGAATTTGGATTGTGATCACTACTTCAACAACAGCAAGGCTCTCAAGGAGGCAATGTGTT

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|29624917|gb|CB629928.1|CB629928
EST:     AAAGGCCAGGCTATAACCATCACAAGAAGGCTGGTGCCATGAACGCATTG                         GTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTC
genomic: AAAGGCCAGGCTATAACCATCACAAGAAGGCTGGTGCCATGAACGCATTGgtaaaagata ... tgattcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTC
EST: gi|58693391|gb|CK082078.1|CK082078
EST:     AAAGGCCAGGCTATAACCATCACAAGAAGGCTGGTGCCATGAACGCATTG                         GTCCGAGTATCTGCTGTACTAAC
genomic: AAAGGCCAGGCTATAACCATCACAAGAAGGCTGGTGCCATGAACGCATTGgtaaaagata ... tgattcacagGTCCGAGTATCTGCTGTACTAAC
EST: gi|29674793|gb|CB671068.1|CB671068
EST:     AAAGGCCAGGCTATAACCATCACAAGAAGGCTGGTGCCATGAACGCATTG                         GTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGAT
genomic: AAAGGCCAGGCTATAACCATCACAAGAAGGCTGGTGCCATGAACGCATTGgtaaaagata ... tgattcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtattaacaaaatatagtgtatgtttaatttttttgctttgttgattcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT
                               tttttttgctttgtt  CT-rich tract
     attaacaaaatatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagataatttctttgatgtttttttggctttccataacctgtactcctgtattaacaaaatatagtgtatgtttaatttttttgctttgttgattcacagGTCCGAGTATCTGCTGTACTAACTAATGCTCCATACATGCTCAACTTGGATTGTGATCATTACATCAACAATAGCAAGGCTATAAAGGAAGCAATGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA