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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtactcctgatgaactcgtgtcccctaggccatcgactttagcctttctgaattatcttgatggattcggttctgcat

Basic information

species Zea mays
transcript GRMZM5G835323_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835323_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g34589.2 (Oryza sativa), 5'ss of exon 3
GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatg-gtactcctgatgaactcgtgtcccctaggccatcgacttta--gcctttctgaattatcttgatggattcggttctgcat-------
||||||||||||||| |||||||||| |||||||||||||||||||||||||||||| |||||||||||||| || |||||||||||||| ||||| ||||| || ||| |       || | |||   |||   |  |    |||     ||||||||  ||  ||    ||| |  | || ||        
GGGATTGAAGAAGGAATTCAGCTACAACAAGATCCTCAAAGATCTCAAGAAAGAGTTTTGCTGCAATGGTACTGTTGTCCAGGACCCAGAGCTTGGCCAGgtgtgtgtaataaccg-aaatttgtggtgcctgatctttacgtttttctatctttctgagctagtttttctgat-caatgcttcactctgtag

upper sequence: GRMZM5G835323_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0177g00100.t01 (Vitis vinifera), 5'ss of exon 3
GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatg-gt----actcct-----gatgaactcgtgtcccctaggccatcgactttagc--ctttctgaattatcttgatggattcggttctgcat------
|||  ||   || || || || |||| |||||||||||| || |||||||| || ||||||||||||||||| || || || ||||| ||||| || ||||| || ||    ||||||     |   |||   |      ||    | |  || |       | |  ||||   || |   |  | ||| |||||      
GGGTCTGCGAAAAGAATTTAGTTACAACAAGATCCTCAAGGACCTCAAGAAGGAATTCTGCTGCAATGGTACTGTTGTTCAAGACCCGGAACTAGGCCAGgtgtgtgtttcaactccttttatggaaaaccatttgtttttattttacctgctgtcataatatgcctaattcgattcacatacgctgttgtgcatttgtag
















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|83279159|gb|DV943167.1|DV943167
EST:     AAGAGTTTTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|21621225|gb|BQ619231.1|BQ619231
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|71767976|gb|DR965913.1|DR965913
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|50332863|gb|CO527989.1|CO527989
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGG--A-                         --------C---AGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|60356711|gb|DN223684.1|DN223684
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|211485134|gb|FL401515.1|FL401515
EST:     AAGAGT-CTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGNACAG                         GCTGCCCGCTATNAG-TCATTCAGCTCCCAGG-TGATCAGAAGAAGAACGT
genomic: A-GAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTAT-AGGTCATTCAGCTCC-AGGGTGATCAGAGGAAGAACGT
EST: gi|4730501|gb|AI649667.1|AI649667
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|71441941|gb|DR822991.1|DR822991
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|211116916|gb|FL407738.1|FL407738
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|78080734|gb|DV509146.1|DV509146
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|5510841|gb|AI857225.1|AI857225
EST:     TCCAGGACCCAGAACTTGGACAG                         GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: TCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|91871868|gb|EB401825.1|EB401825
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|71761988|gb|DR959925.1|DR959925
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|4610125|gb|AI600964.1|AI600964
EST:     GCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: GCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|78112906|gb|DV531300.1|DV531300
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|14204119|gb|BG837796.1|BG837796
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT
EST: gi|60395875|gb|DN228745.1|DN228745
EST:     AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAG                         G-T-C-----AT---TCA----GCTCCAGGGTGATCAGAGGAAGAACGTCT
genomic: AAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 2044

GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 10736

GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9500

GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4537

GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtact ... ggttctgcatGCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATTGAAGAAGGAGTTCAGCTACAGCAAGATCCTCAAAGATCTCAAGAAAGAGTTCTGCTGCAATGGTACAGTGGTCCAGGACCCAGAACTTGGACAGgtatggtactcctgatgaactcgtgtcccctaggccatcgactttagcctttctgaattatcttgatggattcggttctgcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC