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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_T04
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|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|71768983|gb|DR966920.1|DR966920
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|211520835|gb|FL034042.1|FL034042
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|78090964|gb|DV519338.1|DV519338
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520842|gb|FL034049.1|FL034049
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520839|gb|FL034046.1|FL034046
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|211520836|gb|FL034043.1|FL034043
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520838|gb|FL034045.1|FL034045
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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtgcttgcattggtagacatcgacataggtcaccatttggaaatgtgaacaattttacccgttcgttaatctgctgcattctcctgtttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG

- - tgcttgc
- - - - - - - - - - - - - - - -gtcacca
- - - - - - - - - - - - - - - - - - - - - - - - -gaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgctg