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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacagtcttgtatgtctgatactctgatgcctcaaacgtttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG

Basic information

species Zea mays
transcript GRMZM2G006452_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 18
----ttacagtcttgtatgtctgatactctgatgcctcaaacgt-ttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
     | || | ||    |  |  | ||||  |       | || ||| || ||  || |    || |  |   ||          ||  |||| |   ||||||||||||||||| || ||||||||||| || |||||||||||||||||||||||||| |||||||||||||| |||
ggctcttcattgttaacagggttgttctcttgtaaaagctatgtcttgaactgaaagtgtctaaagggaaagagttgatg-----ttgtggttcctatactgcagGTTGATGCTGCCCTAGATCTGAGCCATACACAAAACATTGGTAGAATGATCAAGGCGCATTTTCCGCACTCCCAG

upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
ttacagtcttgtatgtctgatact-ctgatgcctcaaacgtttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
 || | |  ||  ||| |||||    |||||  |  | | ||       | |  ||    |  |||      | ||| ||     ||||       ||||||||||||| ||||||||| |||||||||| |||||||| || |||||||| |||||||| |||||||||||||||
ataaatttatgcttgtttgataggattgatggattgagcattctcgataaattaataggcattgtggttgggt-caaatgttaattgtttcattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG

upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
ttacagtcttgtatgtctgatac-tctgatgcctcaaacgtttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
 || | || ||  | | |||||  | |||||  |  | | ||       | |  ||    | ||||      | ||| ||     ||||       ||||||||||||| ||||||||| |||||||||| |||||||| || |||||||| |||||||| |||||||||||||||
ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggttgggt-caaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG

upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
----------------------------------------------------------ttacagtcttgtatgtctgatactctgatgcctcaaacgtttgta--cggattgtat-gctgagagtgaccattttcaactgactgatg--ttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
                                                          | ||       |  || |   ||  |||| | | ||| |||   |  |  ||  | | | ||||  |||  |  |   |   | | |||  ||  |  |   ||||||||||| ||||||||||| |||||||| || ||||| || |||||||| ||  ||||||| || || || |||
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttg-acagtgat-cttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagag-aagtcatgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG

upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
------------------------------------------------------ttacagtcttgtatgtctgatact--ctgatgcctcaaacgtttg-tacggattgtatgctgagagtgaccattttcaactga-----ctgatg--ttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
                                                      |||   |     || | |     |   | |||  ||  | ||     || |||| |    |   |    | | |    |  ||     || |||  || |   | | ||||||||||| ||||||||||| || ||||| || ||||| || |||||||| |  |||||||| || ||||| |||
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatgtggaacactgattttgcattacaatcagcgagtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG

upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 18
----------ttacagtc-ttgtatgtctgatactctgatgcctcaaacgtttgtacggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
          | | |||| || |   |   ||| | || |||   | || | |       ||| ||  | | |  ||   | | ||| | | |    || ||       |||| |||||||| |||||| | || ||||||||||||||||| |||||||| ||  | ||||| || || || |||
gttttgttcatgaaagtcattttcccttctatattttgttgctctatacttctac-----ttgcatattcaaatgga---tctgcaaataatttgattttgt---tgatagGTCGATGCTGCCCTTGATTTAAGTCACACTCAAAACATTGGAAGAATGATTAAATCCCATTTCCCACATTCCCAG

upper sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
ttacagtcttgtatgtctgatactctgatgcctcaaacgtttgtacggattgtatgc-tgagagtgaccattttcaactgactgatgttcgtg---ctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
  | | ||    || ||      |||| |||        ||   |   |  ||||   |    | |||  |  | ||  || |  ||| | ||      ||||||| || |||||||||||| |||| ||||| || ||||| |||||||||||||| |  || ||||| ||||| |||
-cataatcc---atttcaacctttctgttgcagatctatttaagagaaacggtataaattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG

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|211018645|gb|FL458046.1|FL458046
EST:     CCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATT
genomic: CCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATT
EST: gi|60343263|gb|DN210236.1|DN210236
EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|211376362|gb|FL264047.1|FL264047
EST:     CCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: CCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|22473074|gb|BU037554.1|BU037554
EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|60342993|gb|DN209966.1|DN209966
EST:     ACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: ACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|78021476|gb|DV489863.1|DV489863
EST:     CACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: CACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|60342521|gb|DN209494.1|DN209494
EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|6031321|gb|AW076178.1|AW076178
EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
EST: gi|26457122|gb|CA828705.1|CA828705
EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggattgtatgctgagagtgaccattttcaactgactgatgttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
                       attttcaa  TA-rich tract