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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttactgcactgttctcccgcccttctttcttactccatctttcgacatatataaataaatgtgtgtgctatcacgttcccactctctgaatgtctgatcattaacttgttgaccttgttcttaaggtaaagctactcactcactcccatctagtactgcaattgattcttgtccccccgtgtatgccttctgcag

Basic information

species Zea mays
transcript GRMZM2G174990_T03
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174990_T03 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 13
GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttactgcactgttctcccgcccttctttcttactccatctttcgacatatataaataaatgtgtgtgctatcacgttcccactctctgaatgtctgatcattaacttgttgaccttgttcttaaggtaaagctactcactcactcccatctagtactgcaattgattcttgtccccccgtgtatgccttctgcag
|| || || || || |||||||| ||||| |||||||| ||||||||||||| ||| ||  |||||||||| |||||||||||| ||    ||||  | | ||| |||||| ||       | || |||     |  |  |    |   ||   ||||    | | |  ||| ||   ||                                                                                               
GCTCTCTATGAAGCCCTGATGCGGCAGGACGAGCTGCTTGCGTACATTGACAAGCAAGATATGATCAAGTTTCGTgtacgttacagct---ttcttacactctt-tttcttgcta------ttgagataagagcagcagagc-catctaattctgttct---tttatatatgcctttgcag----------------------------------------------------------------------------------------------
















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|211055318|gb|FL438696.1|FL438696
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|16380026|gb|BI993269.1|BI993269
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|211483107|gb|FK977834.1|FK977834
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGA-GTTCTGCTTTCTA-GATCTGACCATGGAGCAGC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTT-CTAAGATCTGACCATGGAGCAGC
EST: gi|31997891|gb|CD661822.1|CD661822
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|31611996|gb|CD568618.1|CD568618
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|71426246|gb|DR807296.1|DR807296
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTTTGCTTTTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|60672515|gb|DN475220.1|DN475220
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|60336722|gb|DN203695.1|DN203695
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|60336887|gb|DN203860.1|DN203860
EST:     AGGATGAGCTGCTGGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|13557670|gb|BG549026.1|BG549026
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC

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), 48 (downstream exon)
Score: 47

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 205

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttactgcactgttctcccgcccttctttcttactccatctttcgacatatataaataaatgtgtgtgctatcacgttcccactctctgaatgtctgatcattaacttgttgaccttgttcttaaggtaaagctactcactcactcccatctagtactgcaattgattcttgtccccccgtgtatgccttctgcag

- - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT