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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtgcttgcattggtagacatcgacataggtcaccatttggaaatgtgaacaattttacccgttcgttaatctgctgcattctcctgtttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG

Basic information

species Zea mays
transcript GRMZM2G060564_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060564_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 2
--aatgtgcttgcattggtagacatcgacataggtcaccatttggaaatgtgaacaattttacccgttcgttaatctgctgcattctcctgtttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG
   || | ||    |   |     | | || |  | | ||||| ||||||| ||   ||||||||  |  || ||||  | ||||| ||  ||||||||||||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||
atgatattctgtggtgtctttgagtaggcagaa-ttagcatttagaaatgttaatt-ttttacccagtatttgatcttttacattcccccctttctgttcagTGGACCATGTGTGTCATACATGCTTCGCAAAAGGGCTCTGTATAATGACATGTCAAG

upper sequence: GRMZM2G060564_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G63830.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------aatgtgcttg----cattggtagacatcgacataggtcac-catttggaaatgtgaacaattttacccgttcgttaatctgctgcattctcctgtttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG
                                      |||   ||      ||  ||| | |     |   | |  || ||   | | || |    |      | |     || || |   || | |  |||   |  ||||||||||| ||||| ||||||||||| | ||| || || |||||||||||||||||
gtaagttgttgttgatctatttgcttttagggtttcgttgtatctgagattgtttttaggcttatttttgcttgattcaattttgagtctgtattcatggttttggttacatatttgatttgttatacattttgaatgtagTGGACCTTGTGTGTCATACATGCTTCGGAGAAGAGCACTTTACAATGACATGTCAAG
















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|211520836|gb|FL034043.1|FL034043
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|37416319|gb|CF645810.1|CF645810
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGCACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520841|gb|FL034048.1|FL034048
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520834|gb|FL034041.1|FL034041
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520840|gb|FL034047.1|FL034047
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211397639|gb|FL034039.1|FL034039
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211397637|gb|FL034037.1|FL034037
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|148930645|gb|EC872835.2|EC872835
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520833|gb|FL034040.1|FL034040
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211397638|gb|FL034038.1|FL034038
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520838|gb|FL034045.1|FL034045
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520842|gb|FL034049.1|FL034049
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|78090964|gb|DV519338.1|DV519338
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520835|gb|FL034042.1|FL034042
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|101396680|gb|EB820265.1|EB820265
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACGTGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520837|gb|FL034044.1|FL034044
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|76011810|gb|DT938980.1|DT938980
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520839|gb|FL034046.1|FL034046
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgaacaattttacccgttcgttaatctgctgcattctcctgtttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG
                     cgttaat  putative branch site (score: 4)
                                    ttctcctgtttctgtt  putative PPT
     aacaatttta  TA-rich tract