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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgtacgatcttaagtactccattctgtatagcctaggctgaatggactacacatgcgagcttagccttgtgtttgttatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA

Basic information

species Zea mays
transcript GRMZM2G041797_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------------------------------gtatgtgctgt-acgatcttaagtactccattctgtatagcctaggctga---atggactacacatgcgagcttagccttgtgtttgttatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA
                                                                                        ||     | | || || ||  | | |  | | || | |    | |||     ||| | ||| | |  |||||||    |||   |||  |  |||||| ||||||||||||||||| || || ||||| |||||||| ||||||||||| || || ||||| || || || |||| |||||| ||||| ||||||||
gtacgtatataatatgaaaatagcttctcccactgttgcttgaagatattattaacatctaattgacaataaagaaaaacatctgagttaaaaattattaccatgttgggaagtgtaatatgca-aattcatgctagtttatgcattactc-tatgagcttatgtatgt-catgtgcttgtgcagCCATTTCTATTGGGAGGAGGTATGCAAGGACAGATGAGATCGGTGTTCCATTCGCGGTAACAGTTGACTCTGCGACAAGCGTGACAATCCGGGAGAGGGA
















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|149005033|gb|EE039558.2|EE039558
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|5706200|gb|AI941976.1|AI941976
EST:     CGCCAAGGCATTANCAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|211345391|gb|FL470871.1|FL470871
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|22715363|gb|BU197723.1|BU197723
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|26456132|gb|CA827715.1|CA827715
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGT
EST: gi|5525550|gb|AI861443.1|AI861443
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|5901205|gb|AW042305.1|AW042305
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|23199576|gb|BU582141.1|BU582141
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|5650342|gb|AI920702.1|AI920702
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|5847270|gb|AW000349.1|AW000349
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
EST: gi|78022253|gb|DV490640.1|DV490640
EST:     CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTG                         CAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT
genomic: CGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 58

GTGTTCCCCCTCGTCAAGAATCAAGAGTTTGATGCTGCTGCCAAGGAAATCGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 46

GTGTTCCCCCTCGTCAAGAATCAAGAGTTTGATGCTGCTGCCAAGGAAATCGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA


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

GTGTTCCCCCTCGTCAAGAATCAAGAGTTTGATGCTGCTGCCAAGGAAATCGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 54

GTGTTCCCCCTCGTCAAGAATCAAGAGTTTGATGCTGCTGCCAAGGAAATCGCCAAGGCATTAACAACTGCTGGTATCTCACACATTATTGATACTACTGgtatgtgctg ... tatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaggctgaatggactacacatgcgagcttagccttgtgtttgttatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA
                                            ttatctt  CT-rich tract
                                        tttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctgtacgatcttaagtactccattctgtatagcctaggctgaatggactacacatgcgagcttagccttgtgtttgttatcttgcagCAATTTCTATTGGGAGGAGATACGCGAGGACCGATGAGATTGGTGTTCCATTTGCCGTGACAGTGGATTCGGCAACAAACGTGACTATCCGAGAGAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG