Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG

Basic information

species Zea mays
transcript GRMZM2G073077_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073077_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------------------------tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG
                                                                                                                             | ||||||||||| |||| |||||||||||||||||| | || || ||||| || || |||||||||||||||||   
attcccacagtgaatttcactttaattaaactgtataacaataataagattaaaatagccttcacctgtctagtactaagataaatgtgtaatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAGATGCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATAC---
















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|211149119|gb|FL417450.1|FL417450
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211466169|gb|FL380588.1|FL380588
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211180868|gb|FL091536.1|FL091536
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTRTGAAACTTGAGGACCAAGATGCATTTRAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|56382240|gb|CV984909.1|CV984909
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|76013187|gb|DT940357.1|DT940357
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|50327367|gb|CO522493.1|CO522493
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211221445|gb|FL389599.1|FL389599
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|5555446|gb|AI881397.1|AI881397
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211521193|gb|FL395748.1|FL395748
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGCCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211045344|gb|FL397284.1|FL397284
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211123288|gb|FL412657.1|FL412657
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGCCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211403085|gb|FL391554.1|FL391554
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|23357704|gb|BU645353.1|BU645353
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211368876|gb|FL402356.1|FL402356
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|76013186|gb|DT940356.1|DT940356
EST:     CATGCTGTTGTT                         TTGAGTGTGAAAC-TGAGGGACCAAGATGCATTTGAACGTGATTTCTGTCA
genomic: CATGCTGTTGTTt ... tTTGAGTGTGAAACTTGA-GGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACAT
EST: gi|211290626|gb|FL412730.1|FL412730
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|21987255|gb|BQ778783.1|BQ778783
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|71428537|gb|DR809587.1|DR809587
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|9255128|gb|BE345596.1|BE345596
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211160049|gb|FL415236.1|FL415236
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|32910449|gb|CF015261.1|CF015261
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211311554|gb|FL415801.1|FL415801
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGNGAAACTTGAGGACCAAGATGCATTTGAACGAGATTTTCTGTCA
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTT-CTGTCAGCTA
EST: gi|32910399|gb|CF015211.1|CF015211
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211257382|gb|FL426637.1|FL426637
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211204476|gb|FL397886.1|FL397886
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211202662|gb|FL427928.1|FL427928
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211244803|gb|FL372839.1|FL372839
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211343978|gb|FL410639.1|FL410639
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAAMTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211488047|gb|FL401996.1|FL401996
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|19057828|gb|BM736495.1|BM736495
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211071747|gb|FL413442.1|FL413442
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211259601|gb|FL417871.1|FL417871
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|74240003|gb|DT647917.1|DT647917
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211196531|gb|FL380888.1|FL380888
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGCCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|60358231|gb|DN225204.1|DN225204
EST:     TGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: TGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|56382239|gb|CV984908.1|CV984908
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211238673|gb|FL405238.1|FL405238
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211144477|gb|FL393223.1|FL393223
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|120480690|gb|EH210959.1|EH210959
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211207035|gb|FL397427.1|FL397427
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211273315|gb|FL388187.1|FL388187
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|71331372|gb|DR802521.1|DR802521
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|148947219|gb|EC892573.2|EC892573
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG
EST: gi|211119379|gb|FL414341.1|FL414341
EST:     GGGACATTTATGAGCATGCTGTTGTT                         TYGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAG
genomic: GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATG

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: 26 (upstream exon), 49 (downstream exon)
Score: 595

GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG


Block sizes: 26 (upstream exon), 49 (downstream exon)
Score: 710

GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 565

GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG


Block sizes: 26 (upstream exon), 49 (downstream exon)
Score: 434

GGGACATTTATGAGCATGCTGTTGTTt ... tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tTTGAGTGTGAAACTTGAGGACCAAGATGCATTTGAACGTGATTTCTGTCAGCTAAAGCCTTATTACATGGATACATG

- - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA