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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaacatgacaaacttcttttacatttcttttaattgtattgtacatatatgtcaatgcaccttcaaactcatcagcattttcagtactcttatgatctttagtctgtcatagttcatgcttagactccttactcatttcatggttccgctattctccatcag

Basic information

species Zea mays
transcript GRMZM2G161728_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161728_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g49070.1 (Oryza sativa), 5'ss of exon 4
ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaacatgacaaacttcttttacatttcttttaattgt------------------attgtacatatatgtcaatgcaccttcaaactcatcagcattttcagtactcttatgatc-tttagtctgtcatagttcatgcttaga---ctccttactcatttcatggttccgc-tattctccatcag------
 ||||||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||||||||| ||| | |||||||||||||| ||   |  ||||| | ||   |   ||||| || |                  ||  | |   | ||  | || | |||||||||  ||  |  ||    |  |||||  ||   |||  |  |||   |||||| ||  |    ||  |||| |||||||  |||| | | ||||   |         
GTCTGCTAATATCGGAGTATTTCTTTGCTTAAAGTGTGGAGATGTACATAGAGCACTTGGACCAGACGTTTCAAAGgttatttggaccacaggaacttttctt-tgtcagttttagttcttacaaaataagaaaaaaaatcctcctgttgtgcaactgtatcttcaaacttttctcccattatt-tcttcttagaattacttacacaatcagtattcatgtttgcagctttcactactgatttcattcttccacctgttctttttttttgtcag

upper sequence: GRMZM2G161728_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 5'ss of exon 3
ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaacatgacaaacttcttttacatttcttttaattgtattgtacatatatgtcaatgcaccttcaaactcatcagcattttcagtactcttatg-atctttagtctgtcatagttcatgctta---gactccttactcat---ttcatggttccgctattctccatcag
 || |||||||||||||||||| | |||||||||||| | | ||| || ||    |||||   | | |||||||||||| |    ||          |||||    |||   || ||  | | ||  | || || || || |       | | |   |  ||   | || | || || || | |  |||  |     |  | ||||    |    || |   |   || || |||   | | | ||||    
GTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAGgttgt---gactctttgcttctctttctagttttggtttatctt-tggtgaaaatttgccattggattcc---attaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagtttt-caactttccag---
















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|74234877|gb|DT642791.1|DT642791
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211285005|gb|FL330934.1|FL330934
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATAT
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATAT
EST: gi|148970443|gb|EE021294.2|EE021294
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|148982152|gb|EE028182.2|EE028182
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211110591|gb|FL338760.1|FL338760
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211369326|gb|FL186711.1|FL186711
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211029006|gb|FL358137.1|FL358137
EST:     GCTTAAAATGTGGAGATGTTCATAAGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTC
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTC
EST: gi|211369327|gb|FL186712.1|FL186712
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211531455|gb|FL327595.1|FL327595
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACT
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACT
EST: gi|211381172|gb|FL350978.1|FL350978
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211255468|gb|FL340105.1|FL340105
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGT
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGT
EST: gi|78079893|gb|DV508305.1|DV508305
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211230929|gb|FL338421.1|FL338421
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211005122|gb|FL358937.1|FL358937
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAC-G                         -TTTTATCTGTAACTTTGGATGATTGGTCTGACTAGTGATATCGACTCCAT
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGA-TAGTGATATCGACTCCAT
EST: gi|211437933|gb|FL338199.1|FL338199
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211531838|gb|FL338634.1|FL338634
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTC
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTC
EST: gi|211467079|gb|FL315616.1|FL315616
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211268265|gb|FL364919.1|FL364919
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCCTGTAACTTTGGATGA
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATC-TGTAACTTTGGATGA
EST: gi|211369324|gb|FL186709.1|FL186709
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|91050811|gb|EB161229.1|EB161229
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|149008427|gb|EE040587.2|EE040587
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|71327521|gb|DR800373.1|DR800373
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211006794|gb|FL317953.1|FL317953
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGA
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGA
EST: gi|211354852|gb|FL354351.1|FL354351
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGA
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGA
EST: gi|211118991|gb|FL350362.1|FL350362
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTC
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTC
EST: gi|76287384|gb|DV026952.1|DV026952
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
EST: gi|211284991|gb|FL330460.1|FL330460
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAR                         GTTTTATCTGTAACTTTGGATGA
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGA
EST: gi|211510664|gb|FL361518.1|FL361518
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGA
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGA
EST: gi|211286672|gb|FL320843.1|FL320843
EST:     GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG                         GTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG
genomic: GCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATG

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: 375

ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATGGTTGAGGTTGGTGGAAACTCATATGCAAATTCAATTTATGAGGCTTTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 391

ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATGGTTGAGGTTGGTGGAAACTCATATGCAAATTCAATTTATGAGGCTTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 417

ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATGGTTGAGGTTGGTGGAAACTCATATGCAAATTCAATTTATGAGGCTTTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 267

ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaa ... tctccatcagGTTTTATCTGTAACTTTGGATGATTGGTCTGATAGTGATATCGACTCCATGGTTGAGGTTGGTGGAAACTCATATGCAAATTCAATTTATGAGGCTTTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAGgttatttgaacatgacaaacttcttttacatttcttttaattgtattgtacatatatgtcaatgcaccttcaaactcatcagcattttcagtactcttatgatctttagtctgtcatagttcatgcttagactccttactcatttcatggttccgctattctccatcag

- - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - GAGATG