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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG

Basic information

species Oryza sativa
transcript LOC_Os05g06430.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G138616_T01 (Zea mays), 3'ss of exon 1
gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
                        ||   ||  ||||   |    |   |||  |  |  |||  ||| |||| || |||||||| |  ||||   |||||||  |||||||||||||||||| ||   ||  |   |||| |||||||| |||| |||||| ||||| |||||||||||||
-----------------------gttggtta--taaagccaagcga---aatcgctttggaattcatttgttg-ttgtgtagGCTAGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGTTGTTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G008647_T04 (Zea mays), 3'ss of exon 1
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttc---tgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
    ||  |      | |  |||    |||    | | || || |   | |     ||  ||  | ||| ||  ||  ||    |||||||| |  ||||   |||||||  |||||||||||||||||| ||   ||| |   |||| |||||||| |||| |||||| ||||| |||||||||||||
gttggttataaagcca-agcgaaatcgctttgg-aatcaagttgatgaattatggatctgatgcattctgttcatttgttgctgtgtagGCTAGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCTGTTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC217311.3_FGT007 (Zea mays), 3'ss of exon 2
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttc---tgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
    ||  |      | |  |||    |||    | | || || |   | ||    ||  ||  | ||| ||  ||  ||    ||||||||||  ||||   |||||||   ||||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||
gttggttataaagcca-agcgaaatcgctttgg-aatcaagttgatgaattctggatctgatgcattctgttcatttgttgctgtgtagGCTGGGCTTGTGCCAAGCTTGAACCCTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 8
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttct---gtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
    ||  |      | |  |||    |||    | | || || |   | ||    |   ||  | ||| ||  ||  || |   |||||||||  ||||   |||||||  |||||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||
gttggtcataaagcca-agcgaaatcgctttgg-aatcaagttgatgaattctggatttgatgcattctgttcatttgttgttgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 5
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttc---tgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG-----
    ||  |      | |  |||    |||    | | || || |   | |     ||  ||  | ||| ||  ||  ||    |||||||| |  ||||   |||||||  |||||||||||||||||| ||   ||| |   |||| |||||||| |||| |||||| ||||| |||||||||||||     
gttggttataaagcca-agcgaaatcgctttgg-aatcaagttgatgaattatggatctgatgcattctgttcatttgttgctgtgtaggctagGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCTGTTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTGCTAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G170845_T01 (Zea mays), 3'ss of exon 4
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttc---tgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
    ||  |      | |  |||    |||    | | || || |   | ||    ||  ||  | ||| ||  ||  ||    ||||||||||  ||||   |||||||  |||||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||
gttggttataaagcca-agcgaaatcgctttgg-aatcaagttgatgaattctggatctgatgcattctgttcatttgttgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 6
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttc---tgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
    ||  |      | |  |||    |||    | | || || |   | ||    ||  ||  | ||| ||  ||  ||    |||||| |||  ||||   |||||||  ||||||||||| |||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||
gttggttataaagcca-agcgaaatcgctttgg-aatcaagttgatgaattctggatctgatgcattctgttcattttttgctgtgtagGTTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGATGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 8
----gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggt-tgcttctgt--agGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
    ||  |     ||     ||     ||  |  |  || || |   | ||    ||  ||  | ||| ||  | || | ||||  |||||||  ||||   |||||||  |||||||||||||||||| ||   ||| ||  |||| |||||||| |||| |||||| ||||| |||||||||||||
gttggttataaagctaagcgaaatcgctttggaagc--aagttgatgaattctggatctgatgcattctgttcatgtgttgctgtgtagGCTGGGCTTGTGCCAAGCTTGAATCCTCTTGTGAAGGAGTTTCTCAATGCTGCTGATGACAAGCGGAAGGAAGTCCTCTCTAAAATAGAAGAGGATGTTG

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|163925853|gb|EG714953.1|EG714953
EST:     AGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: AGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58672427|gb|CK061113.1|CK061113
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|163922917|gb|EG712742.1|EG712742
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58653948|gb|CK042628.1|CK042628
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58676547|gb|CK065234.1|CK065234
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|11026410|gb|AU163011.1|AU163011
EST:     GGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: GGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|86482186|gb|CI124819.1|CI124819
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58690891|gb|CK079578.1|CK079578
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|86513133|gb|CI155766.1|CI155766
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|163927756|gb|EG710536.1|EG710536
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|87017864|gb|CI273886.1|CI273886
EST:     ATGAGAAATGTGGAACCACCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58683615|gb|CK072302.1|CK072302
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
EST: gi|58675064|gb|CK063751.1|CK063751
EST:     ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAG                         GCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA
genomic: ATGAGAAATGTGGAACCAGCCGTGATTCAAAGGGTCAGCTTACTTCAGAGgtagtgcttt ... gcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacttaaatttacataatccaattccaatataatctattggttgcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG
                                           ttgcttct  CT-rich tract
     ttaaatttacataatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgcttttatatagaaggtacttaaatacttaaatttacataatccaattccaatataatctattggttgcttctgtagGCTGGCATTGTCGAAAGCTTGGCTCCTCTTGTGAAGGAGTTCCTTGGTGCAGCAAATGATAAGCGGAAAGAAGCCCTCTCCAAAATGGAAGAGGATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG