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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcgaatgcaaccggtagcaatgttcatccagtttagtctttagtgcccccccacccccccaaaaaaaatgtttgtctaatatatcgttgtcgtgacag

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 15
CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcgaatgcaaccggtagcaatgttcatccagtttagtctttagtgcccccccacccccccaaaaaaaatgtttgtctaatatatcgttgtcgtgacag
  ||||| || ||||| | ||| ||  |||| ||||||||| |||||||||||   |||||||||||||||| |||   ||||||  | ||||||   |  | ||   |   || ||    |  |  |       | || ||     ||| |||| | | |    ||  ||||
GGGCACCGTTTAAGAAGTTTGCTTCATTGCGAGATGAGTGGTCCCTCAAGAACCATTACATCAGCCCTGgtacgtggacatgcaatagctagcaag--tagtgcaaaatga-ctataacagcaacatag------agaacaatgacatgtttaatttcttg----cgaaacag

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 15
CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcgaatgcaaccggtagcaatgt-tcatccagtttagt-------ctttagtgcccccccac-----ccccccaaaaaaaatgtttgtctaatat---atcgttgtcgtgacag---------------------------------------------------------------------------
 ||| || ||||| |||| |||||| ||||| ||||||||||| ||||||||   ||||||||| ||||||| |        |   |    |||  |  |  |||| | || |       | | |||| |            ||    ||  | |      |   |||     |  |      ||| ||                                                                           
GTGCTCCATTCAAAAAATTTGCATCTATGCGGGATGAGTGGGCTCTCAAGAATCAATACATCAGTCCTGgtaagctaccgctctttctactgcagggccttctccactctaatgaactttcatcagtgactgattgaatttgccttttaagtagaggacgagatgaatgccaaactgaaactttgaaagcttagtaaaaatttcaatttctgcttggagacaatctcttctactaacacaacactcttattgatttgattgcag
















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|29544787|gb|CB605395.1|CB605395
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATG
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATG
EST: gi|67014773|gb|CO443522.1|CO443522
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|67014279|gb|CO443028.1|CO443028
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|9742494|gb|BE518657.1|BE518657
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|211286470|gb|FL080391.1|FL080391
EST:     TGCATCGATGCGTGATGAGTGGGCCATCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGT
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGT
EST: gi|211286474|gb|FL080395.1|FL080395
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|16377178|gb|BI991814.1|BI991814
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|149083928|gb|EE173305.2|EE173305
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|211286476|gb|FL080397.1|FL080397
EST:     TGCATCGATGCGTGATGAGTGGGCCATCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|211286473|gb|FL080394.1|FL080394
EST:     TGCATCGATGCGTGATGAGTGGGCCATCAAGAACAGATWCATCAGCCCTG                         GCCCCATCCARTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACT
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACT
EST: gi|10450958|gb|BE924882.1|BE924882
EST:     TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
EST: gi|211286478|gb|FL080399.1|FL080399
EST:     TGCATCGATGCGTGATGAGTGGGCCATCAAGAACAGATACATCAGCCCTG                         GCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA
genomic: TGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGA

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: 290

CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGATGCTGGAACTCGGTGCTGCGCTATAGAGATGCGTCCTTTACTTTGTTCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 162

CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGATGCTGGAACTCGGTGCTGCGCTATAGAGATGCGTCCTTTACTTTGTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGATGCTGGAACTCGGTGCTGCGCTATAGAGATGCGTCCTTTACTTTGTTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 220

CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcga ... gtcgtgacagGCCCCATCCAGTTCAGTGGCCCTGGAAGTAATGACTCGAACCATACTTTGATGCTGGAACTCGGTGCTGCGCTATAGAGATGCGTCCTTTACTTTGTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCACCTTTCAAGAAATATGCATCGATGCGTGATGAGTGGGCCCTCAAGAACAGATACATCAGCCCTGgtatgtgcgaatgcaaccggtagcaatgttcatccagtttagtctttagtgcccccccacccccccaaaaaaaatgtttgtctaatatatcgttgtcgtgacag

- - - - - - - - - - - - - - - - - - - - - - -  AAGAAC