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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgctgatcgtttcgccgcgatttttctttcgctatctggttatactttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG

Basic information

species Zea mays
transcript GRMZM2G106795_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 1
--------------------gtccgctgatcgttt-cgccgcgatttttctttcgctatctggttatactttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
                     |  | |  ||           || | |||| |   | | ||| | |  | |    ||||| | ||  | |||||      ||   | |   |||||||  |||||| ||||||||||| ||||||||||| || |||||||||||| ||||||||||||| |||||||||||  | ||||||||||| |||||||
gtatgggtgatttttcttttttttgtttgtcaaaagtaagaagaatattctctttttttttgggtgtgttcttcgagaacttcttgattgatttt------tgctctgtgacgcttgctctttagGTCGTGATGCTTGGGCTGGATGCCGCGGGCAAAACCACCATCCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 1
gtccgctgatcgtttcgccgcgatttttctttcgctatctggttatactttcaatgaact--gcctgtatcattttgttgattgtggttttctgc--ttgcttg--ttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
         | ||||  |   |  |  || | |    |||    |||  | |  ||| ||  || ||  |     |  | | | |  |||| | |  ||| | |  ||||||||||||||||||||| ||||| || || ||||| || ||  |||||||||| || || || || ||||| || |||||||| || || |
---------ttgtttttcttagtctcatcatccatcttctaaccatagatcct-tgatctttgcatgagtttccgtacttactttttttttttacatttgttgggattagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 1
-gtccgctgatcgtttcgccgcgatttttctttcgctatctggttatactttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
 || || | ||  ||  |   |   || || |   | ||||  | ||  ||         |   || |  | |||    | |    |||  ||  |     ||||||||||||||||||||| ||||| || || ||||| || ||  |||||||||| || || || || ||||| || |||||||| || || |
tgttcgttaatacttgtgtttcttattctcatcatccatcttctaatcattgattcttgatctatgcacgagtttccgtacttacatttgttgggt-----ttagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 1
gtccgctgatcgtttcgccgcgatttttctttcgctatctggttatactttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttg--ttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
      |  || |        |  | |  | |   ||| |  | ||  ||||  |         |      |||  | |||    || |    |   |||  |||||||||||||||||| |||||||| || |||||||| |||||  |||||||  |||| || || || |||||||| ||||||||||| ||||
------tattcttgagtttatgcctgtattcttaatatttattcatgatttctctatgtccttcgagcttattttcttatttaaattattaattgagttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTG

upper sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 1
gtccgctgatcgtttcgccgcgatttttctttcgctatctggttatactttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
|| |    |    || |   |||| ||| ||| | ||       ||||    |    | | |||||    |   |    || |     |     |   ||  ||||||||||||||||| | ||||| || || |||||||||||| | || ||||| || || || ||| || |||| || |||||||| ||||
gttcatctac--atttgaatcgatgttt-tttagatagaattccatacaggaagcacatt-cctgtgatttaccgagatttcttacgattcttgtatctgccagGTTGTGATGCTTGGTTTAGATGCAGCAGGCAAAACCACCATCCTCTATAAGCTTCACATTGGAGAGATTCTGTCCACCGTTCCCACCATTG

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|211066465|gb|FL305325.1|FL305325
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211091310|gb|FL335551.1|FL335551
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|74241061|gb|DT648975.1|DT648975
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|101398288|gb|EB821017.1|EB821017
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211076278|gb|FL377992.1|FL377992
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066463|gb|FL305323.1|FL305323
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211069201|gb|FL305331.1|FL305331
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211497259|gb|FL426008.1|FL426008
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066466|gb|FL305326.1|FL305326
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066464|gb|FL305324.1|FL305324
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTNAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211069203|gb|FL305333.1|FL305333
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTNAAACCACCATCTTGTASAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066470|gb|FL305330.1|FL305330
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066462|gb|FL305322.1|FL305322
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066467|gb|FL305327.1|FL305327
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211069202|gb|FL305332.1|FL305332
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
EST: gi|211066468|gb|FL305328.1|FL305328
EST:     AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGG                         GTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG
genomic: AGGCGTTCCGCAAGCTGTTCGATGCCTTCCTCGGCACCAGCGAGATGAGGgtccgctgat ... tgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG
                        tgttgat  putative branch site (score: 4)
                                    ttttctgcttgctt  putative PPT
                tatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgctgatcgtttcgccgcgatttttctttcgctatctggttatactttcaatgaactgcctgtatcattttgttgattgtggttttctgcttgcttgttagGTTGTGATGCTTGGTCTGGATGCCGCCGGTAAAACCACCATCTTGTACAAGCTGCAAATCGGGGAGGTTTTGTCGACTGTTCCCACGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC