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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccataatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT

Basic information

species Oryza sativa
transcript LOC_Os08g45240.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 2
cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccat----aatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
    |      | |    ||||||       |||   ||| | |    ||  | |||||||||   |   |||    ||||||   ||  || |||| |||||||||||| |||||||||| |||||||| || ||||| ||||||||||||||||||||||||||||||||| | |||| |||||| ||||| |||||||   
--ctctaagtagcgaggcttatgtcagtcattgtgtgcagcatttggcat--gcatttcttgattttatacattcttaatttgcctttgcactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAGACTAAAGGTTATGGATTTGTGAGCTTTTCAAACCCTACTGACTTGGCTGCAGCAATAAAAGAGATGAATG---

upper sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 2
cctccctccct-gtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccat----aatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
  ||  |   | |||    ||||||       ||    ||| | |    ||  | |||| ||||  ||   |||    ||||||  ||  ||| |||| |||||||||||| |||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| || |||| |||||| ||||| |||||||   
--tctataagtagtgaggcttatgtcagtcattgcgtgcagcacttggcat--gcattttttgattctatacattcttaatttgc-ctcgtactctttatttcagGTTGTTAGAGATAAGAGGACTGGCAAAACTAAAGGCTATGGATTTGTGAGCTTTTCAAACCCTACTGATCTGGCTGCAGCAATAAAAGAGATGAATG---

upper sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 3
------cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccataatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
         |    | | | ||  |||||| ||  |  || ||  ||| | | |  || | | |    ||  | |  || |   |||  |||| | |  ||   |||||||  |||| ||| | ||||| ||||||||||| |||||||||||||||||| | || ||| ||||||||||||  ||  |||||||||||||||   
ctaagcaaacttaacttttattatttatgtgtttgtg-gtgcat-gtatttccttgtgatgtgttgacagtgttgtgattaag-gtatgtttatcttgact---agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATG---

upper sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------cctccctccctgtgtttgttatgttttcttatgta----cacagtagtacttattggtatttcttgaggctggcc-------ataatttgtacttttaccctttctt--tcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
                                                                   | |   ||  | |  |  | |  ||||  | || |    || ||| ||   |||| || | |||| | |  || |       || |  || | || |      ||||    |||||||  |||||||  | ||||| ||||||||||| |||||||||||||||||| | || ||| ||||||||||||  ||  |||||||||||||||   
gtaagtggattactcatctagctcaaatgatttttatgtttaggaatgattgtggtgcttctgtgagcatttttctatttcctcttcagatttttgtttgaagggacagagttgttaatatttgtgtatcttaacgtaggtcttgcttaatgacctgaagttatgtttgatcttgtctagGTTGTCAGAGATAAACGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG---

upper sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 3
--cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccataattt--gtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
     |   |     |||| |||| |     | |||        ||| ||  | ||| |   |       |   | |||   |||  |||| | |  ||   |||||||  |||| ||| | ||||| ||||||||||| |||||||||||||||||| | || ||| ||||||||||||| ||  |||||||||||||||   
ctaaacaaacttaacgtttattatttaagtgtttgtg-gtgcatgtatttccttgtaatgagttgacagtgttgtgattaaggtatgtttatcttgact---agGTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATG---

upper sequence: LOC_Os08g45240.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 3
cctccctccctgtgtttgt-tatgttttctta-tgtacacagt-agtacttattggt--atttcttgaggctggcca-taatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
      |  ||||| |  |  |||| |  | | | |    | | || |||| |   |  |||| ||  || |||  | ||||   || ||   | | |||   ||||||||  |||||||| | || || ||||| |  || | ||| ||||| |||||||| |||||| | |||||||| | |||| ||||||||||||| |   
----aattgctgtgatcttgcatgtctgttaaatatttggaatgaggacttgtcatttcattttttatggttggaaactaatgcatagttcctcacattc--acagGTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG---

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|33684393|gb|CF312632.1|CF312632
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|58599191|gb|CK009719.1|CK009719
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAG
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAG
EST: gi|88368173|gb|CI575055.1|CI575055
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|38475426|gb|CF959559.1|CF959559
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|86829522|gb|CI286725.1|CI286725
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAA
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattggtatttcttgaggctggccataatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT
                              tttgtacttttaccct  CT-rich tract
                          ataatttgtactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctccctccctgtgtttgttatgttttcttatgtacacagtagtacttattggtatttcttgaggctggccataatttgtacttttaccctttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
cctccct
- - - - - - tgtttgt
- - - - - - - - - - - - - - - -tgtacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggctggc