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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcag

Basic information

species Zea mays
transcript GRMZM2G304362_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 11
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaaccacctgt--tcttttctgtaactagttgatatgtaacaaatggttttatcttttcag
 ||||| || ||||| ||||| ||||||||||||||||| |||||||||||  |||||||||||||||||||||| |||||||| |||||||||||||||||| |||||| |   || |||    || | ||       ||  || || ||  |  ||  |||| |  || |  || |    |||||||||
CGCAAAAAGATCAAATATGCGGCACAGGCCAATTGGCATTGGTGTTCAAGGGTTGGCAGATACTTTCATATTACTTGGCATGCCATTTGATTCACCAGAGgtaacttttcctagttcagtaatatagtagtactagttagtagtccttcctacacttaactgatgtaaaaaatgtgatcccctcttttcag

upper sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 11
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaacc--acctgttcttttctgtaactagttgatatgta-acaaatggttttatcttttcag
 |||||  |||||||| | || ||||| |||||||| ||||| || || || || || |||||||||||| |||| |||||| | ||||||||||||||||||  | | | | |     |        |||      |  ||| |||   | ||| ||||| |  || | |  ||||               
TGCAAAACGGTCAAACTTACGGCACAGACCAATTGGTATAGGAGTACAGGGTCTTGCTGATACTTTCATACTACTTGGCATGGCATTTGATTCACCAGAGgtaaatctacttctgaggctgctgttatattcgttgtatttgtgcttcagtctaa-tagttcacttggatattaatgcag------------

upper sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA06G15350.1 (Glycine max), 5'ss of exon 11
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcag
 |||||  |||||||| |||| ||||| |||||||| || || || || || || || |||||||||||| | || |||||| | ||||||||||||||||||  | | |     ||    |||     |||   |   ||| | ||        |  |||||  | ||    | | ||||        
TGCAAAACGGTCAAACTTGCGGCACAGACCAATTGGTATTGGAGTACAGGGTCTTGCTGATACTTTCATACTCCTTGGCATGGCATTTGATTCACCAGAGgtaaatctac----ttcaagggcttctgttta--tattcgttttatttccacttcatatgatagtttacttg-gatattatgcag----

upper sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 5'ss of exon 11
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcag
 ||||| |  |||||||||||||| || || ||||| || ||||| |||||||| |||||| | || ||  | || || ||||| |||||||| |||||||||   ||   ||      |     | | |  |  |  |  | ||         ||  || | |  | ||  |   ||| | |  ||||
TGCAAAAACTTCAAACATGCGTCATAGACCTATTGGTATTGGTGTACAAGGCCTTGCAGATGCATTTATCCTCCTTGGAATGCCATTTGATTCTCCAGAGgtagacttgttttgaattatgatcaatcttggaaaatataatttt-------gttatctgttcttaagcagtttaatttgt-tactcag

upper sequence: GRMZM2G304362_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 5'ss of exon 11
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgt--agctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcag-----
 ||||| ||||||||| ||||||| || || |||||  | || ||||| || || |||||||| ||||| || || |||||| | ||||||||||||||||||    |   |||    |   |   |  ||||   | |||||   || |  | | || ||    ||| | || |  ||| | || || |      
TGCAAAAAGGTCAAACTTGCGTCATAGACCCATTGGTCTTGGAGTTCAGGGTCTTGCAGATACCTTCATTTTGCTTGGCATGGCATTTGATTCACCAGAGgtaaagctaattttgcagggcaaatacttcattgtgctcctgtggattccaatga-tacttagc-tgtgataattaatttga-ctattgactgcag

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|211165343|gb|FL103231.1|FL103231
EST:     GCCTGGCAGATACTTTCATATTATTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|211165341|gb|FL103229.1|FL103229
EST:     GCCTGGCAGATACTTTCATATTATTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|32933128|gb|CF037940.1|CF037940
EST:     GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|211102666|gb|FK948700.1|FK948700
EST:     GCCTGGCAGATACTTTTATATTACTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATRCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|33098100|gb|CF058060.1|CF058060
EST:     GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|32931387|gb|CF036199.1|CF036199
EST:     GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATAT-T-CGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|32930756|gb|CF035568.1|CF035568
EST:     GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
EST: gi|211165338|gb|FL103226.1|FL103226
EST:     GCCTGGCAGATACTTTTATATTACTGGGCATGCCGTTTGATTCACCAGAG                         GCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG
genomic: GCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTG

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: 523

AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 97

AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 123

AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttc ... atcttttcagGCTCAACAGTTGAATAAGGATATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAAGAGGTCAAACATGCGTCACAGGCCAATTGGCATAGGTGTTCAAGGCCTGGCAGATACTTTCATATTACTGGGCATGCCGTTTGATTCACCAGAGgtaccttttcatttctccgtagctcagcattaaccacctgttcttttctgtaactagttgatatgtaacaaatggttttatcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT