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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttacatcagaaattttttttcttcatattacagtatcagctagtcaatccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 11
----gttattttacatcagaaattttttttctt--catattacagtatcagcta-gtcaatccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG
    ||| ||    |  || |||    |||| |    | ||| |  || |  |   |  ||      ||||     |||  |  | | ||||  ||||  ||   ||| ||| | |||||||||||||||||||||| || | ||||||||  ||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||| ||||
gtttgtttttcactacaaggaatgacatttcctattttgttatacaattatttttatgcatttctgtaattactggatatctggcttaattttgcatttgattacttccatacgtagGCTGGACAAAAACGTGGAAGATTACATGTAAATCCAGAAGAAGATGAGCAACCGAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATTTCAG

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 11
gttattttacatcagaaattttttttcttcatattacagtatcagctagtcaatccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG
      || |    |   |||| |||    || |||  || | | ||| |   |      |  ||   ||||||    |||         | |||  ||| || |  |||| ||| ||||| || |||||| ||||| ||||||| ||||||||||| ||||| ||||||||||| ||| | || || || || | ||||||||||||||
-----gttgctatggtgtttttattttaggatgttaaggtgttatctattttgtttgattacattgtgtataataagaatg--------ctaaatcttttttacaaacagGTTGGCCAAAAGCGAGGAAGGATGCTTATAAATCTGGAAGAAGATGAGCAACCTAAGAAGAAAGTGCGATTGGGGAGTCCTGCTACTCAGTGGATATCAG

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 11
gttattttacatcagaaattttttttcttcatattacagtatcagctagtcaatccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG
                  || |  |  ||||||||    | ||      |||  |||        |  ||  ||||   |  |||    |    |  | |  |||   ||| ||| ||||| || ||||| |||||  ||||| | ||||||||||| || |||||||||||||| ||| | || ||||| || |  |||||||||||||
-----------------gttgtgatgtttcatatttttatttctttacttcagaccaga------tggtaggattccttttctttattgtaatgtcttctgcataactagGTTGGGCAAAAGCGGGGAAGATTGCTCATAAATTTGGAAGAAGATGAGCAGCCAAAGAAGAAAGTACGATTAGGTAGCCCTGCGACCCAGTGGATATCAG

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|4714662|gb|AU055779.1|AU055779
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
EST: gi|58609933|gb|CK037966.1|CK037966
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
EST: gi|58609726|gb|CK037759.1|CK037759
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAGTCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTT
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTT
EST: gi|66914155|gb|CX101003.1|CX101003
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
EST: gi|702121|gb|D48412.1|D48412
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGGAAGATGNACA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAG-AAGATGAACA
EST: gi|5005377|gb|AU070539.1|AU070539
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacccaattttaatataattcacatgatttgacattgaatggtttctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG
                                          tttctat  CT-rich tract
     aattttaatataattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattttacatcagaaattttttttcttcatattacagtatcagctagtcaatccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA