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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttactttctgcttttcaataacttacgctttgtgtcatgatatttatgttcatgatgaagatttctgtttgtttcattctcaaattcctatgcattgaccttaatagctaaagcatgctccctacctgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC

Basic information

species Zea mays
transcript GRMZM2G304362_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 12
gttttactttctgcttttcaataacttacgctttgt-gtcatgatatttatgttcatgatgaagatttctgtttgtttca-ttctcaaattcctatgcattgaccttaatagcta-aagcatgctccctacctgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC
       ||| |||||||    |  | ||  ||| | ||      |||||      |  | |    |   |||||  | | || |    |   |||  |       || |   |  |||  || |  ||| |  ||||  ||||||||||||||||||| |||||| ||||||| |||||| ||||||||||||||||||||||| ||   || ||||| ||||||||  ||||||| ||||
-----gttttttgcttttactaatgtcactttttttagtagctgaatttaccaatttatttattggtgtagtttgactaaattgttggttggatatcaacaagtaatattctttctaaggctgttttctatccacttttcagGGCATTCTCCAACCTGATATGTGGAATGTAGTTCCATCTGACAGATGGAACTGGCCATCTCTACGGAGTACTATTTCTAAAGTTGGATTAAGAAACTCTC
















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|32932369|gb|CF037181.1|CF037181
EST:     ATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: ATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|32934636|gb|CF039448.1|CF039448
EST:     CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|211165343|gb|FL103231.1|FL103231
EST:     CTGCTAAAGAAGGTCCCTATGAAACTTATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|211165341|gb|FL103229.1|FL103229
EST:     CTGCTAAAGAAGGTCCCTATGAAACTTATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|33098100|gb|CF058060.1|CF058060
EST:     CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAG
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAG
EST: gi|32934774|gb|CF039586.1|CF039586
EST:     CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|5895790|gb|AW037036.1|AW037036
EST:     CTGCTAAAGAAGGTCCCTATGAAACGTATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|29577171|gb|CB617283.1|CB617283
EST:     CCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|32931555|gb|CF036367.1|CF036367
EST:     CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|33094392|gb|CF054386.1|CF054386
EST:     GCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: GCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|32935070|gb|CF039882.1|CF039882
EST:     TCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: TCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|211165335|gb|FL103223.1|FL103223
EST:     CTGCTNAAGAAGGTCCCTATGAAACTTATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|32930756|gb|CF035568.1|CF035568
EST:     CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCT
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCT
EST: gi|211165338|gb|FL103226.1|FL103226
EST:     CTGCTAAAGAAGGTCCCTATGAAACGTATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
EST: gi|32932118|gb|CF036930.1|CF036930
EST:     CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAG                         GGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC
genomic: CTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAAC

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: 379

TATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

TATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

TATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 68

TATATTCGAAACTATCTACTATCATGCTCTGAAAGCTTCTGCTGAACTTGCTGCTAAAGAAGGTCCCTATGAAACATATGAAGGGAGCCCTGTCAGCAAGgttttacttt ... tgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattcctatgcattgaccttaatagctaaagcatgctccctacctgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC
                        agctaaa  putative branch site (score: 68)
                                    ctccctacctgctttc  putative PPT
                   ttaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttactttctgcttttcaataacttacgctttgtgtcatgatatttatgttcatgatgaagatttctgtttgtttcattctcaaattcctatgcattgaccttaatagctaaagcatgctccctacctgctttctagGGCATTCTCCAACCTGACATGTGGGATGTAGTGCCATCTAACAGATGGAACTGGCCATCTCTAAGGGAGACCATTTCAAAAGTTGGGATAAGAAATTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA