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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaacattatcacagtgtgcaatttaatccacattgcttggtcacaactaagcactgattgcatttctctggtgcttggtcgctgcatttaagttttctacttctatgtgcttgcag

Basic information

species Zea mays
transcript GRMZM2G047894_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047894_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g18080.2 (Oryza sativa), 5'ss of exon 3
GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaacatt-atca--cagtgtgcaatttaatccacattgcttggtcacaactaagcactgattgcatttctctggtgctt--ggtcgctgcatttaagttttctacttctatgtgcttgcag
 |  || ||||| || |||| ||| |||||||| ||| | |||||||| ||||||||||||||||||||||||||||| ||||| || ||| |||| |||||| |  || ||| |  |   ||  | |||||| |||||||||| ||||          ||| || ||   ||| ||||||  ||  |||| | | ||   | |||     | | || |  ||||||
AAGGGACGCTGGTTCATATCAGGGATCCCCTGTTTACAATGTGAACTCGATGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaaattgagtagttagcatccaattttatccacattgtttgg----------gcattgtttatctttatctggtatttttggtcacagtatcataatttgtgtatgccatcttattgcag
















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|71428423|gb|DR809473.1|DR809473
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
EST: gi|211511662|gb|FL408088.1|FL408088
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGA-TTGCAGAAAC
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAAC
EST: gi|211199436|gb|FL401716.1|FL401716
EST:     GAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGNAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTAC
genomic: GAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGG-AAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTAC
EST: gi|211223965|gb|FL409228.1|FL409228
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATGG-AGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
EST: gi|211348875|gb|FL413241.1|FL413241
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTCGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAANTGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
EST: gi|78086850|gb|DV515243.1|DV515243
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
EST: gi|211285032|gb|FK988594.1|FK988594
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
EST: gi|71325385|gb|DR799370.1|DR799370
EST:     TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAA                         AGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACT

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), 49 (downstream exon)
Score: 111

GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACTTGTGGATTGTATTATTCATATGACAGGGATTTGACACTAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 62

GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACTTGTGGATTGTATTATTCATATGACAGGGATTTGACACTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACTTGTGGATTGTATTATTCATATGACAGGGATTTGACACTAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 120

GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaac ... gtgcttgcagAGAAGGGATGAGGCATACTTCATGTCTCTCCTGAGAATTGCAGAAACTACTTGTGGATTGTATTATTCATATGACAGGGATTTGACACTAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaacattatcacagtgtgcaatttaatccacattgcttggtcacaactaagcactgattgcatttctctggtgcttggtcgctgcatttaagttttctacttctatgtgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC