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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattttcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt...

Basic information

species Zea mays
transcript GRMZM2G000393_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g07905.2 (Oryza sativa), 5'ss of exon 9
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattttcctgttaggagatactacctcccgttcacaaata--tatgacactgttgattt
||| |||||||||||||||||||| |||||||| ||||||||||||||||||||||| || |  ||| |||    ||      ||| || |||| ||  |  | ||      || |       | | |  ||||  | ||   ||  || | |
GGGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaactaacatattcaaggtccttgccatttgtctatt-atcctaatattcatct-tagtgttgggtgattagcaataattctgtgtctagtggtgt

upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G14000.1 (Glycine max), 5'ss of exon 9
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcat-----tctcctgaattagtttatt-cattttcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt
|||  | | ||||||||||||||| |||||||||||||| |||  |||| ||| ||| |  | || | | | |       | |  ||| ||| ||||||  ||| | |||  | ||  | | |  |     ||  ||||  ||  || |        
GGGAAAGCCATGGTATGAACCTGATTGGTGGAAATTTGGGGATGAAAAATCgtaagtaatataccttttgcacgagatgatttggtgatttattttattatattatactggaatgatcttcgatgttatcgtcttaaattgataccatttc------

upper sequence: GRMZM2G000393_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT4G32120.1 (Arabidopsis thaliana), 5'ss of exon 9
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattt----tcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt
|||    ||||||||||| |||||||||||||||||||| ||    ||| ||| |||    ||  | ||  |   ||| ||   |||  | |  |  ||     | |  | |    ||||   |  | ||     || |||              
GGGAAGTCAATGGTATGAGCCTGAGTGGTGGAAATTTGGGGACGACAAATCgtaagt-gtcttatacctcataggtcttctcgtttatgtcaagcccttgtgaccttcgttgtgtgtactcagtttctttgttcgatttatttag----------

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|32928477|gb|CF033289.1|CF033289
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|71435122|gb|DR816172.1|DR816172
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|60338589|gb|DN205562.1|DN205562
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|71436236|gb|DR817286.1|DR817286
EST:     GGCCACCAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|50323552|gb|CO518678.1|CO518678
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|4775973|gb|AI664976.1|AI664976
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|78021331|gb|DV489718.1|DV489718
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|32846895|gb|CD986576.1|CD986576
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAACTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTTTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTC-ACCTC                         G
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacag-
EST: gi|33091019|gb|CF051013.1|CF051013
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTC-ACCTC                         G
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacag-
EST: gi|60346760|gb|DN213733.1|DN213733
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|71426993|gb|DR808043.1|DR808043
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|32929367|gb|CF034179.1|CF034179
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGGTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|61119808|gb|DN560769.1|DN560769
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|60344825|gb|DN211798.1|DN211798
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|149005473|gb|EE040028.2|EE040028
EST:     GGCCACCAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTTTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|71772159|gb|DR970096.1|DR970096
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|149096404|gb|EE182138.2|EE182138
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|110200892|gb|EC882789.1|EC882789
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|24765385|gb|CA400544.1|CA400544
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|21828587|gb|BQ703271.1|BQ703271
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|78093004|gb|DV521378.1|DV521378
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|211130920|gb|FL136658.1|FL136658
EST:     GCCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: G-CCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|60346466|gb|DN213439.1|DN213439
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|148940752|gb|EC885572.2|EC885572
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|15082759|gb|BI389443.1|BI389443
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|113703856|gb|EE681360.1|EE681360
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
EST: gi|5124017|gb|AI745858.1|AI745858
EST:     GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAAC                         GTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC
genomic: GGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaat ... ataaaaacagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCCAACAATGGTATGAACCTGAGTGGTGGAAATTTGGAGATTCAAAAACgtgagttaatttccatcttctcattctcctgaattagtttattcattttcctgttaggagatactacctcccgttcacaaatatatgacactgttgattt

- - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - -  GGAGAT