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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgcatctctttcctgatatgtcagtgggaaatgcatctatgataagcaggttgcaactacatatatttcttctattgttctctgactgttcatgtggttattatttatgtctatacag

Basic information

species Zea mays
transcript GRMZM2G049091_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049091_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 5'ss of exon 5
TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtat-ttccgcatctcttt-----cctgatatgtcagtgggaaatgcat---ctatgataagcaggttgc------------aactacatatatttcttctattgttctc--tgactgttcatgtggttatt---atttatgtctatacag
||||||||| | |||  ||||||| ||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||| |||   || | |||     |   || | | ||||  |||  |||    || ||||      |||             ||| ||| ||||||  |  |||  ||||  ||  || |  |||| || ||     ||   | ||| |||
TAGGGATCGCAGGGAACTGGAAAATATTATATTCAAGCTTTTTGAAAGACAGCCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatattcttgatttatttggcgtctctatttttaagtgaaaaaaacattggttaagatactttatttgtggtgttcctatgaacaacaaatattttattcattactctcaatggttgctt-tgtgattgtttgtgcttcgttttatgcag

upper sequence: GRMZM2G049091_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 5'ss of exon 5
TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgcatctctttcctgatatgtcagtgggaaatgcatctatgataagcaggttgcaactacatatatttcttctattgttctctgactgttcatgtggttattatttatgtctatacag
 |||||||||  |||  ||||| | ||||| ||||||||||||||||||||||| || |||||  |||||  ||| || ||||| || || || || | |||||       ||| ||   || |     | ||   |||   |||| | |||      | |      | ||||  |||    |||  |   |   ||||||| | |                   
AAGGGATCGTGGGGAACTGGAAGATATTATGTTCAAGCTTTTTGAAAGGCAACCTAACTGGGCCTTAAAGCAGCTAGTCCAAGAGACAGATCAACCTGCGgtat------gtcttttgattgcttcagtattgcataattgttctaagttaatggctctcctttggaacatatcacttgc-ctgtgatgaaatgcttcatgttgatg------------------
















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|60394867|gb|DN227736.1|DN227736
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|32935815|gb|CF040627.1|CF040627
EST:     AACCCAATTGGGCACTAACGGCACTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|71330940|gb|DR802278.1|DR802278
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAAGAGATATTGAACGATCTCTGTGTGTATAATAA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAA
EST: gi|71321696|gb|DR797540.1|DR797540
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|149087888|gb|EE287172.2|EE287172
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCACTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|110532526|gb|EE036710.1|EE036710
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|47962465|gb|CN845174.1|CN845174
EST:     TGGGCACT-AAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: TGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|148999712|gb|EE036711.2|EE036711
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTTCTGA-GGAGATATTNGA-CGATCTCTGTGTGTATAATAAACGAG
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTT-CTGAAGGAGATATT-GAACGATCTCTGTGTGTATAATAAACGAG
EST: gi|18661513|gb|BM501437.1|BM501437
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|91869041|gb|EB400255.1|EB400255
EST:     ACCCAATTGGGCCCTAAAGGCGCTGGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTTTGAAGGAGATATTGAACGATCTCTGTGTGTTTAATAAACGAGGA
genomic: ACCCAATTGGGCACTAAAGGCGCT-GGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|60341247|gb|DN208220.1|DN208220
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|78078665|gb|DV507077.1|DV507077
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|6307892|gb|AW163859.1|AW163859
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|120480832|gb|EH211048.1|EH211048
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTTTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|211422720|gb|FL461576.1|FL461576
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|166409992|gb|EG133122.1|EG133122
EST:     AACCCAATTGGGCACTAAAGGCACTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGA
EST: gi|78078666|gb|DV507078.1|DV507078
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|71596151|gb|DR906902.1|DR906902
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACCGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|6056902|gb|AW091307.1|AW091307
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
EST: gi|78083456|gb|DV511849.1|DV511849
EST:     AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAG                         CAATTTTTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA
genomic: AACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGA

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), 44 (downstream exon)
Score: 62

TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGACCAAACCAGGGAACTCATGAGCTTAAGCCAGAGTACAAGAAATCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 80

TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGACCAAACCAGGGAACTCATGAGCTTAAGCCAGAGTACAAGAAATCCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 81

TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGACCAAACCAGGGAACTCATGAGCTTAAGCCAGAGTACAAGAAATCCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgc ... gtctatacagCAATTTCTGAAGGAGATATTGAACGATCTCTGTGTGTATAATAAACGAGGACCAAACCAGGGAACTCATGAGCTTAAGCCAGAGTACAAGAAATCCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGGATCGTACGGAGATGGAAAACATTATATTCAAGCTTTTTGAAAGGCAACCCAATTGGGCACTAAAGGCGCTGGTGCAAGAAACTGACCAGCCAGAGgtatttccgcatctctttcctgatatgtcagtgggaaatgcatctatgataagcaggttgcaactacatatatttcttctattgttctctgactgttcatgtggttattatttatgtctatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA