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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactattactgttgttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacag

Basic information

species Zea mays
transcript GRMZM2G032367_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 7
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactattactgttgttgtttatccct-gtacttttgaattgtggggctaggactaa-------agtttgaccacttata-cttccatcacag
 ||||| |||||||||||||||||||||||||| |||||||||||||| |  |||||||||||||| ||||| |||||||||||||| ||||||||||||||||  |  || ||  ||||||   | ||   | || |||  ||| ||| ||| | |||       ||  |||    |   | | || | |||||
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTCCTGCCACTGAAGCCCAGgtaagtttctaatgc-gttgttgggctcttacagttgtgacatgttgggttagcattaagggcctaagcatgattgttgtcatcctctaccacag

upper sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G06700.2 (Glycine max), 5'ss of exon 6
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgta----aactattactgttgttgtttatccctgta---cttttgaattgtggggctag---gactaaagtttgaccacttatact-tccatcacag
 || || || ||||| |||||||| || || |||||||| || ||||| |||||||| ||||| || ||||| |||||||||||||| || ||||| ||||||    |  |  | |||  |   | |      |||   ||| | ||   ||||  | |   || |  || |      ||  || | |   |  |||
TTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTCCTGCTACAGAAGCTCAGgtattaaatttgcttctggaggaatatggtttagtaaatcttcttaaaaatgggatttgatagaatctagctcattttctcttaatgtttgttgcag

upper sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 6
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt----actgttgttgtttatccctgtacttttgaa--ttgtggggctaggactaa--agtttgaccacttatacttc-catcacag-----
|||||| || || |||||||| || || || || ||||| || ||||||||||||| ||||||||||||||| ||||||   || || || || || ||||| |  | |     |||     | |     | |  |  |||     || |||  ||     |    ||| | |  |  || ||||  | | || |     
CTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCCCCGCCACAGAGGCACAGgttatttttcctccacttaaaatataagaacataaatctttatgccttatggtactgtcctttctcagtgtcatgatataaactttactttacggtgcag

upper sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 5
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactat----tactgttgttgtttatccctgtacttttgaattgtg--gggctaggactaaagtttga-ccacttatacttccatcacag---------------------------
|||||| || || ||||||||||| || || || ||||| || |||||||| |||| |||||| || ||||| ||||| ||||||||||| ||||| ||||| |  | |    | ||   |    | ||      ||  |  | || |    |  | |  ||    | |||  || |||||    | | |                              
CTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTCCTGCAACAGAAGCACAGgttagttttcctctgcttaagaaaataatttgcagaccataaagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcag

upper sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 6
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactattactgttgttgtttatccct---gtacttttgaattgtggggctaggact---aaagt-ttgaccacttatacttccatcacag-----------
|||||| || ||||||||||| ||||| || || ||||| || ||||||| |||||| ||  |||||||||| |||||||| |||||||| || || |||||    | | |       |  ||    ||   || ||| | || |||      |    |   || || ||    | ||     ||   || |            
CTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttcatctactctaattgcaacttgggtgcttcttaactgtaattgcatctttttcaaggtgttagaaaattgagtgtcttccataattctggtgcag

upper sequence: GRMZM2G032367_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactattactgtt-----gttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacag
||| || || || ||||||||||| || ||||| |||||||| |||||||  ||||| |||||||||||||| |||||||| ||||| || ||||| || ||||  |  |    ||     ||  |||||      | |||   | ||  ||  | | |  |  | |   |   |  ||       |||||
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcctgtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactgatattctcatcttaacgttggcacag

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|71763205|gb|DR961142.1|DR961142
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|5006059|gb|AI712121.1|AI712121
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|14245130|gb|BG873712.1|BG873712
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|76290228|gb|DV029796.1|DV029796
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|32938109|gb|CF042928.1|CF042928
EST:     CCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: CCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|71757789|gb|DR955726.1|DR955726
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|5608164|gb|AI901831.1|AI901831
EST:     AGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: AGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|211323657|gb|FL286663.1|FL286663
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|37386374|gb|CF630373.1|CF630373
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|32939220|gb|CF044039.1|CF044039
EST:     CCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: CCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|29947382|gb|CB816627.1|CB816627
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|78026464|gb|DV494851.1|DV494851
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG

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: 177

CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactattactgttgttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC