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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 6
gtcattgttcatc--atgcc-attgattcttccagcgc--ctcatgtgaaaaactcaattacagaa---tttatttttgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
||   ||||  |   ||||  ||| | |  |||   ||  || ||| |||  |   ||| |  | |   |||  | ||| | ||||||||||||||||| || |||||||||||||| |||||||| |||||||| |||||||| |||||||||||||| ||||||||||| ||||
gttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCCTCAAACAGAGGCCTACTGGGGAAATGTTAACCCAATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 6
------------------------------gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
                               |||   |  ||||| |  ||| |  ||        || | | |  |    | |   ||   |||||||  | | ||||||||||  | |||||||| ||||| || ||||| ||||| |||| |||||| ||| |||| | ||| ||||||||||| ||||| ||||
gttggaaaattgtctttggaaaatgataatttcagcttctatcat-catttggtctttattctttttctttttagtag---agtcttagttcttatttt--attggcagGATTTTACTCACATCAACATCTGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAGGCTATTGGGGCAATGTGAACCCTATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 6
------------------------------gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
                               |||   |  ||||| |  ||| |  ||        || | |       | | |   ||   |||||||  | | ||||||||||  | |||||||| ||||| || ||||| ||||| |||| |||||| ||| ||||   ||| ||||||||||| ||||| ||||
gttggtaaattgtctttggaaaatgataatttcagcttctatcat-cagttggtctttattctttttcttcttg-----ttagtcttagttcttatttt--attggcagGATTTTACTCACATCAACATCTGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGCTATTGGGGCAATGTGAACCCTATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
----gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaatt--gcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
    |  |||   | ||||   |||  ||   ||||   |     | ||   |||||||    || |||| ||    ||   |||||| ||| | |||||||| || ||||| ||||| ||||| ||||||||||| |||||||||  ||| ||||| ||||||||||| || |
gtttgggatttgacttcattttattcctttaaccaggatc----ataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------gtcattgtt-catca-tgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
                      |    |||  ||||  |   | | | | |    |   |||   |   |   | ||     |   ||  |||      |||||||| |  | || || ||||||||||||||||| |||||  | ||||||||||| || ||||  |||||||| || || ||||| ||||
ccacttaatcggtttggaccgagaagctgtgacatctctagtaataagtatctatgtagctctcatccgatgattaaccttgg---ttgctttatggaggcagGATTCTTCTCACGTCTACCTCTGAAGTTTATGGAGATCCTTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 5
gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaat--tgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
                   || || || |   |   |||   ||  ||   || |  |      ||| |  ||   | ||||||| |  | || |||||||| ||||||||||| |||||||| |||||||| ||||  ||||  |||||||||||||| || || || |
------------------gttaat-ctcctctcttgtcacaagagcaagcaaact--aactcgcattctcaaaccatacagGATTCTACTCACGTCAACCTCCGAAGTTTATGGGGATCCACTGGAGCATCCACAAAAGGAGGAATACTGGGGCAATGTGAATCCCATAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 5
gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaat--tgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
                   || || || |   |   |||   ||  ||   || |  |      ||| |  ||   | |||||||||  | || |||||||| ||||||||||| |||||||| |||||||| ||||  ||||  |||||||||||||| || || || |
------------------gttaat-ctcctctcttgtcacaagagcaagcaaact--aactcgcattctcaaaccatacagGATTTTACTCACGTCAACCTCCGAAGTTTATGGGGATCCACTGGAGCATCCACAAAAGGAGGAATACTGGGGCAATGTGAATCCCATAG

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|149070503|gb|EE158907.2|EE158907
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     GTTATTGGTACCCTGAACATGCTTGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|32838870|gb|CD978551.1|CD978551
EST:     ACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: ACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     TACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: TACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCGTTC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     GTTATTGGTACCCTGAACATGCTTGGACTTGCAAAGAGAGTTGGAGCTAG                         GATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC
genomic: GTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAGgtcattgttc ... tgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaattgcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG
                                     tttattttt  CT-rich tract
                   aaaaactcaattacag  TA-rich tract