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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaactatcttttgcaagcctaagtaaaatggttactgaagcattcgatttgacccctacatttagcgagtatttactttgtgatgtttgtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA

Basic information

species Zea mays
transcript GRMZM2G473001_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 8
agaaactatcttttgcaagcctaagtaaa-atggttactgaagcattcgatttgaccc-ctacatttagcgagtatt-tactttgtgatgtttgtg-ttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA
    |        || || |   | |||| ||       ||  ||||  ||| |||    || | ||    |  ||| || |||||| |||||||| ||| |||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||| ||||| || || |||||||| || ||||||||||
----atggaacagtgtaaactagactaaagataaccttggagccattgaattagacttattagactttttcaaaattataatttgtgttgtttgtggttggcagGCAACACCTGAGACAGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCCAAGAGGAAGCCGAGTGGAGGCATTGAATCACTCCGTGCGATCCCATGGA

upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
agaaactatcttttgcaagcctaagtaaaatggttactgaagcattcgatttgacccctacatttagcgagtatttactttgtgatgtttgtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA
 | ||   |  ||  | |||  || ||   |  |  || || ||    | |||      | |   || |  ||  | |    |   |||||| || | ||||||| || ||    |||||||| |||||||||||||||||| | ||||| ||  | || || |||||||| ||||| || || || |||||||| ||||
-gtaa--gttcttaaccagctcaattac--tcctctcttaaaca----aattgtagttaaaaaagagagtctaagttcaggtttgggtttgtatt-atagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA
















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|211159336|gb|FL360829.1|FL360829
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|211386539|gb|FL356617.1|FL356617
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|211378594|gb|FL355187.1|FL355187
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|211356395|gb|FL313778.1|FL313778
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|211208426|gb|FL344245.1|FL344245
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|211528158|gb|FL316545.1|FL316545
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|13125979|gb|BG316654.1|BG316654
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|13125970|gb|BG316645.1|BG316645
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|50332032|gb|CO527158.1|CO527158
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
EST: gi|33466459|gb|CF243508.1|CF243508
EST:     ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTT                         GCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC
genomic: ATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCC

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: 159

AGAATGGCGAGCCCTTCTTGATGAGATGGCAGTTGTGGCAACTGAGGAATATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

AGAATGGCGAGCCCTTCTTGATGAGATGGCAGTTGTGGCAACTGAGGAATATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

AGAATGGCGAGCCCTTCTTGATGAGATGGCAGTTGTGGCAACTGAGGAATATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

AGAATGGCGAGCCCTTCTTGATGAGATGGCAGTTGTGGCAACTGAGGAATATCGGTCCATTGTCTTCAAAGAGCCACGCTTTGTCGAGTATTTCCGCCTTgtaagtcctt ... gtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgatttgacccctacatttagcgagtatttactttgtgatgtttgtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA
   atttgac  putative branch site (score: 121)
                          tatttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaactatcttttgcaagcctaagtaaaatggttactgaagcattcgatttgacccctacatttagcgagtatttactttgtgatgtttgtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - -tgcaagc
- - - - - - - - - - - aagtaaaa
- - - - - - - - - - - - - - - - - - ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt