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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT

Basic information

species Zea mays
transcript GRMZM2G157675_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 3'ss of exon 1
gtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtact--gatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT
        | ||  |    | |   |  | | |   | |      | |   | ||  |   |  | |  |  | |   | | ||   ||    |    | |  ||  | | | |           | ||||||| |||||||||| |||||| ||||   ||||||||||||||||||||| ||||||| ||||| ||||||||||||||||||||||||||||||||||| 
-------gtaattaagttcttctaatcaagccgatcgatcgaccatctctctctgcatgcaggataggatacaatacaacaaattctgaaattcatttctggttgtgtgtatat--------atgtatgcagGCCGACGTTCTGGAGGATCTGCAAGAGGAAGGACGTGGAGGAGTTCAAGGCGGACCCATACCTAGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAC

upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 3'ss of exon 1
gtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT
|||   |  | ||  |    |||| | |  || | ||     |||  || ||||| | ||||||||   ||   ||  | |     ||      |    | ||    |||    | | |||  ||||||||| |||||||||| |||||| ||||   |||||||||||| |||||||| ||||||| ||||||||||||||||||||||||||||| ||||||||||| 
gtaactaagc-tctctaaacccggttgctgctagctg-----tttaattaatttgatgagggtttttggtgagatgtgagaactgaagaattaacaaatcttgatcttgt----ttgtgtgtgtgtgcagGCCGACGTTCTGGAGGATCTGCAAGAGGAAGGACGTGGAGCAGTTCAAGGCGGACCCGTACCTGGCGACGCTGCTCAACTGCATGCTATGGGTGTTCTAC

upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g08490.1 (Oryza sativa), 3'ss of exon 1
gtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT-------------------------------------------------------------------------------------------
                                                     ||    ||  ||  |  | |  |   |  | |  | ||   |   | |  |  || ||  |||     |  |     ||  || ||||||||||||  ||||   |||||||||  ||| |||||| ||||||  ||||| || ||||||||||| |||||||||| ||| ||||||                                                                                           
----------------------------------------------------gtgtcccggacttgatccgcaacgtggtgggcatcgtcgg--caatgtcatctcctttggcctcttcctctcgccggtgcccaccttctggcggatcatcaagaataaggacgtgcgggacttcaaggcggaccagtacctagccacgctgctcaattgcatgctctagGTTTTCTATGGTCTTCCCATCGTTCACCCCAACAGCATTCTCGTCGTCACCATCAACGGTATTGGCCTCGTCATCGAGGCCGTCTACCTCACCATCTTCT

upper sequence: GRMZM2G157675_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g08030.1 (Oryza sativa), 3'ss of exon 1
-----------------------------gtaggcactcatcgatcg---gtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgt-tctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT-------------
                             |    ||||  || |  |   |  | ||  | | |  |   |     |  |  |       ||  |  |  | ||    ||  | ||    | ||   | |  |   | |||| | |||| |   | | | |    |  |   |  |  || | | |||   | ||| |||| |        |  ||  |  | | ||||| || ||       || | ||||  |   |  |              
gtataggacttcaagacagacccgtacctggccacactgctcaactgtatgctctgggacttttacggtctccccatcgtccaccccaacagcatcctcgtcgtcaccatcaacggcattg-gccttgtcatcgagacctgtctatctcaccatcttcttcctcttctccgacaagAAGAACAAGAAGAAGATGGAAGTGGTGCTAGCGGCGGAGGCTCTCTTCATGGCGGCGGTGGCGCTTGGCGTACTCTTAGGCGTGCACACCCATCAAAGAC

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|211344463|gb|FL201420.1|FL201420
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAACC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|31628388|gb|CD526584.1|CD526584
EST:     GCAATGNCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GNTGACGTTCTGGCGGATCTACAAGGNCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211162574|gb|FL132733.1|FL132733
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|28188031|gb|CB179641.1|CB179641
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGCCGTTCTGGCGGATCTACAAGGCCAAGGACGCGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|37361467|gb|CF602756.1|CF602756
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211342073|gb|FL201410.1|FL201410
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|31627932|gb|CD526360.1|CD526360
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|28188247|gb|CB179857.1|CB179857
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211344467|gb|FL201424.1|FL201424
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAACC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211342078|gb|FL201415.1|FL201415
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211342077|gb|FL201414.1|FL201414
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAACC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|37361336|gb|CF602625.1|CF602625
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211344465|gb|FL201422.1|FL201422
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAACC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211342079|gb|FL201416.1|FL201416
EST:     GCAATGTCATCTCCTTCGGCCTSTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|30160668|gb|CB924397.1|CB924397
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|148934526|gb|EC878568.2|EC878568
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|31628107|gb|CD526445.1|CD526445
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211342076|gb|FL201413.1|FL201413
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|14245092|gb|BG873674.1|BG873674
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211344464|gb|FL201421.1|FL201421
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211342075|gb|FL201412.1|FL201412
EST:     GCAATGTCATCTCCTTCGGMMTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|71317142|gb|DR795259.1|DR795259
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211344466|gb|FL201423.1|FL201423
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|28187755|gb|CB179365.1|CB179365
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211344462|gb|FL201419.1|FL201419
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAACC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|28188001|gb|CB179611.1|CB179611
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|24462465|gb|BM659996.1|BM659996
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|28187611|gb|CB179221.1|CB179221
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
EST: gi|211344460|gb|FL201417.1|FL201417
EST:     GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAACC
genomic: GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT
 tactgat  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT