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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtggattaccacagttaagtagtagtaagaaataggattcgtgggccatacatacaattttaatggtccatatatgattgtgcag

Basic information

species Zea mays
transcript GRMZM2G070605_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g13770.2 (Oryza sativa), 5'ss of exon 8
ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtggattaccacagttaagtagtagtaagaaataggattcgtgggccatacatacaattt-taatggtccatatatgattg---tgcag
||||| |||||||||||||| ||||||||||| || ||||||||||| || ||||| |||||||| || ||||||||||||||||||    |        ||| ||||      ||||  |||||||    || | |||  ||  |  |  ||  |  ||||      |||||
ACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATCgtaagtgtgataaatttggtccaagaagtat-----aatattattcgtgcattatgcttactgttggtgttcctctttccatgaccaacttgcag

upper sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 8
ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtggattaccacagttaagtagtagtaagaaataggattcgtgggccatacata-caattttaatggtc-catatatgattgtgcag
||||||||||| || || ||  | |||||||| ||||| || |||||||||||||| |||||||| || ||  | || |||||||        ||   ||    |    | ||   |  ||||| |    |  | ||| || |||  ||  |  ||| | ||||| | |||
ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTCATTGTCTGCATTCCACCGGCTCTCATTgtaagtgcaa-----catgatttgagatccttgagggttttgattcctaaaactaaaataacagtttccatactttcatgtctgattttacag
















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|32941843|gb|CF046662.1|CF046662
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
EST: gi|32925288|gb|CF030100.1|CF030100
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCA
EST: gi|211010423|gb|FL349731.1|FL349731
EST:     AATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
genomic: AATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
EST: gi|213168524|gb|FM182487.1|FM182487
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
EST: gi|116820056|gb|EC863241.1|EC863241
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCA
EST: gi|32925201|gb|CF030013.1|CF030013
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
EST: gi|91050012|gb|EB160430.1|EB160430
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
EST: gi|32925598|gb|CF030410.1|CF030410
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTG
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTG
EST: gi|32851134|gb|CD990815.1|CD990815
EST:     CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC                         TTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA
genomic: CTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAA

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: 47 (upstream exon), 48 (downstream exon)
Score: 55

ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAAGTAGGCTTGACAAAGTTTGTTAGTGACCTATTCTTGGTTGGACTGTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2327

ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAAGTAGGCTTGACAAAGTTTGTTAGTGACCTATTCTTGGTTGGACTGTTCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 11

ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAAGTAGGCTTGACAAAGTTTGTTAGTGACCTATTCTTGGTTGGACTGTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1175

ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtgg ... gattgtgcagTTTGAAGGGCCCCGGCTAATGCAGCATGGATTCAGTGATGCCATTGCAAAAGTAGGCTTGACAAAGTTTGTTAGTGACCTATTCTTGGTTGGACTGTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATCgtaagtgtggattaccacagttaagtagtagtaagaaataggattcgtgggccatacatacaattttaatggtccatatatgattgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG