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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactcctttcaatggatactctgaatataaagaatttgtctacttttaccatgatgtttccatttagcccatataaatagaagtcaatttcacta...

Basic information

species Zea mays
transcript GRMZM2G461569_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461569_T01 (Zea mays), 5'ss of exon 16
lower sequence: 13114.m00152 (Oryza sativa), 5'ss of exon 5
ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactcctttcaatggatactctgaatataaagaatttgtctacttttaccatgatgtttccat-ttagcccatataaatagaagtcaatttcacta
 |||||||| || || ||||||||| ||||| ||||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||| |||     |||    |||    ||| | | ||  | ||     | | |    |   | | | |    |     ||   | || |||    |      
TTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGGGTGATCCAAATGCTAGCATTCCAACACCTGAACCGgtacggaacttcttcttgagatgagttgagt-tgaaatagttaagagcctgtttggtagagctccaacaccaaaatttagctacaggagttgggtctgaag

upper sequence: GRMZM2G461569_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA11G37250.1 (Glycine max), 5'ss of exon 17
ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgta-tggactcctttcaat--ggatactctg-aatataaagaatttgtctacttttacca-tgatgtttcca-----tttagcccatataaatagaagt----caatttcacta------------------
 || || || || || ||||||||| ||||  | || || ||||   ||||||  |||||||||||||| || ||||| ||||| |||||||||||||| ||| ||   || | |  ||  |||||   |  | |   ||    |     ||||||   | | |   || ||     |||   |||| ||||||||| |    ||| |  ||||                  
GTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGGGTGACCCAAATGCAAGCATCCCAACACCTGAACCGgtaatgttttcatatgcattgggatatgatccagtgccaactggtgccaaacttttttaaatcacactttcaataacttttatccatctaaatagaaatgcttcaactaaactaggaaactcaatcttgtag

upper sequence: GRMZM2G461569_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 5'ss of exon 16
ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatgg-actcctttcaatggatactctgaatataaagaatttgtct---acttttaccatgatgtttccatttagcccatataaatagaagtcaatttcacta
||||||||| || || ||||||||| ||||  |||| || |||| ||||||||||||||||||||||||||| ||||||||||| || ||||||||||| |||    | |  | | |||| ||       |||   ||||          | |   | ||   ||||| ||||  |  |||   |  | |   |||||| |  |
ATCTTTCTTTGGGGCAAAACCAGAAATGGTGATAAAAGGTGGTGTAATTGCATGGGCTAACATGGGTGATCCAAATGCTAGCATCCCTACACCTGAACCGgtaaattatttttattaatgaatttataacatactgagaagggaaaagaaagtggaaacaccctgtttacatt--gttcatg--agcaaattgcaatttaatga

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|211109878|gb|FL467775.1|FL467775
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|32834778|gb|CD974456.1|CD974456
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|32932810|gb|CF037622.1|CF037622
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|213172274|gb|FM186421.1|FM186421
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|213172803|gb|FM187184.1|FM187184
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|76011931|gb|DT939101.1|DT939101
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|31358228|gb|CD442585.1|CD442585
EST:     ATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAGCGACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: ATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAAC-ACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|32834768|gb|CD974446.1|CD974446
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|32835420|gb|CD975098.1|CD975098
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|213170447|gb|FM190520.1|FM190520
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
EST: gi|211090509|gb|FK961026.1|FK961026
EST:     CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCT                         GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT
genomic: CATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAAT

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: 58

ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAATTCAATTGCATTTGTGAGCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 73

ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAATTCAATTGCATTTGTGAGCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 82

ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAATTCAATTGCATTTGTGAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactc ... tctgatgcagGTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAATTCAATTGCATTTGTGAGCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGGGTGATCCCAATGCTAGCATTCCAACACCTGAACCTgtatggactcctttcaatggatactctgaatataaagaatttgtctacttttaccatgatgtttccatttagcccatataaatagaagtcaatttcacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatagaa