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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcattaacagtagtttgaggctttgagcataattgaagtttcctttattccacttcagtgtttcttgatcgaactgatgttatccttttgactttacag

Basic information

species Zea mays
transcript GRMZM2G079256_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 4
GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcattaacagtagtttgaggctttgagcataattgaagtttcctttattccacttcagtgtttcttgatcgaactgatgttatccttttgactttacag--------------
||  ||||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| || |  |||  ||| ||  ||          || || | ||||  | || |||| ||||||||| | || | |||    | | |||    ||   |   |               
GCACTGAACATATTTGAGACAAGCTTGAGGCGTGGGAAGTTTGACGAATCACGAAAgtgtgttc-ctaagtgtacttgcagt---------tatttaatgttttgtgtagtccatttcagtgttccatgctggaatgattatcatctccatggtgtctgactacctttgttgcag

upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 4
GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat-taacagtagtttgaggctttgagcataattgaagtttcctttattccacttcagtgtttcttgatcgaactgatgttatccttttgactttacag
||  | || ||||||||||||||||||||||||||||| || ||  | |||||   || ||  | |  ||||  |  |||     ||     |||| | |  ||  ||| |||||     || | |   |                                
GCACTTAATATATTTGAGACAAGCTTGAGACGTGGAAAATTCGACCAGTCACGAGTgtaaggacttacaacatgatcttgtctggttttatgtaatgggacattaattt-ttccatccatgtatattcag--------------------------------
















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|211312412|gb|FL116820.1|FL116820
EST:     A-CATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCCTATGG
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGG
EST: gi|211312423|gb|FL116831.1|FL116831
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|32865280|gb|CF004962.1|CF004962
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|60345537|gb|DN212510.1|DN212510
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|21987661|gb|BQ779189.1|BQ779189
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCA
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCA
EST: gi|32907240|gb|CF012053.1|CF012053
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|78076466|gb|DV504900.1|DV504900
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211312417|gb|FL116825.1|FL116825
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGA
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGA
EST: gi|211314440|gb|FL116834.1|FL116834
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGA
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGA
EST: gi|32908286|gb|CF013099.1|CF013099
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|67011703|gb|CO440452.1|CO440452
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|87156317|gb|DY401106.1|DY401106
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211314439|gb|FL116833.1|FL116833
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGNTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAA
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAA
EST: gi|32911684|gb|CF016496.1|CF016496
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGTACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|71332949|gb|DR803501.1|DR803501
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211314448|gb|FL116842.1|FL116842
EST:     ACATATTTGAGACAAGCTTGAGACGTGAAAAAGTT-GATGA-TCACGGAA                         GCTACCTGATGGATCTCCTATGGAGATTGC
genomic: ACATATTTGAGACAAGCTTGAGACGTGGAAA-GTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGC
EST: gi|211312419|gb|FL116827.1|FL116827
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCC
EST: gi|211314447|gb|FL116841.1|FL116841
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCCTTATGGAGATTGCTAAAGTATATCCACTGGGAC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTC-TTATGGAGATTGCTAAAGTATATCCACTGG-AC
EST: gi|211312418|gb|FL116826.1|FL116826
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGAC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGAC
EST: gi|211314443|gb|FL116837.1|FL116837
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|22819573|gb|BU499663.1|BU499663
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211314444|gb|FL116838.1|FL116838
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTAT
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTAT
EST: gi|31356068|gb|CD440425.1|CD440425
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211312415|gb|FL116823.1|FL116823
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|26559923|gb|CA832158.1|CA832158
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211310397|gb|FL116818.1|FL116818
EST:     AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAA                         GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGC
EST: gi|211314445|gb|FL116839.1|FL116839
EST:     AACATATTTGA-ACCAGCTTGAGACGTGAAAAGTTTGATGAATCACG-AA                         GCTACCTGATGGATCTCTAATGGAGATGGCTAAAGTATATCCACTGGGAC-
genomic: AACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGG-ACG

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: 199

GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT


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

GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 61

GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcat ... gactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTTGAACATATTTGAGACAAGCTTGAGACGTGGAAAGTTTGATGAATCACGGAAgtgagtgcattaacagtagtttgaggctttgagcataattgaagtttcctttattccacttcagtgtttcttgatcgaactgatgttatccttttgactttacag

- - - - - - - - -  CAAGCT