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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_T01
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|71449020|gb|DR830070.1|DR830070
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520834|gb|FL034041.1|FL034041
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|78078643|gb|DV507055.1|DV507055
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|91048377|gb|EB158795.1|EB158795
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|50336576|gb|CO531702.1|CO531702
EST:     CCTACTGTTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|76011810|gb|DT938980.1|DT938980
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|101399172|gb|EB821460.1|EB821460
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71330287|gb|DR801905.1|DR801905
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|74234235|gb|DT642149.1|DT642149
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|26456824|gb|CA828407.1|CA828407
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|76284637|gb|DV024205.1|DV024205
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|148953515|gb|EE153023.2|EE153023
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520833|gb|FL034040.1|FL034040
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|149095487|gb|EE181140.2|EE181140
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|20512803|gb|BQ280001.1|BQ280001
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71447386|gb|DR828436.1|DR828436
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|148930645|gb|EC872835.2|EC872835
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520842|gb|FL034049.1|FL034049
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|76014988|gb|DT942158.1|DT942158
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|78090964|gb|DV519338.1|DV519338
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|148937865|gb|EC882083.2|EC882083
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|148949975|gb|EC895492.2|EC895492
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520835|gb|FL034042.1|FL034042
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|74245152|gb|DT653066.1|DT653066
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|149089290|gb|EE178503.2|EE178503
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|101396680|gb|EB820265.1|EB820265
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACGTGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71321160|gb|DR797280.1|DR797280
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71311330|gb|DR791989.1|DR791989
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|78107038|gb|DV525456.1|DV525456
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520837|gb|FL034044.1|FL034044
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71312763|gb|DR792909.1|DR792909
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|211520839|gb|FL034046.1|FL034046
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71768464|gb|DR966401.1|DR966401
EST:     CCTACTGCTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|71315575|gb|DR794393.1|DR794393
EST:     CCTACTGCTGCCTCGCGCTGT-G-G                         T-GACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
EST: gi|50337111|gb|CO532237.1|CO532237
EST:     CCTACTGTTGCCTCGCGCTGTGGTG                         TGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT
genomic: CCTACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 22 (upstream exon), 49 (downstream exon)
Score: 188

ACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG


Block sizes: 22 (upstream exon), 49 (downstream exon)
Score: 390

ACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG


Block sizes: 22 (upstream exon), 49 (downstream exon)
Score: 215

ACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG


Block sizes: 22 (upstream exon), 49 (downstream exon)
Score: 466

ACTGCTGCCTCGCGCTGTGGTGgtgagccatc ... ttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgaacaattttacccgttcgttaatctgctgcattctcctgtttctgttcagTGGACCTTGCGTGTCGTACATGCTTCGCAAAAGGGCTCTCTACAATGACATGTCAAG
                     cgttaat  putative branch site (score: 466)
                                    ttctcctgtttctgtt  putative PPT
     aacaatttta  TA-rich tract