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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttgcctgtatagcattctgattgttgccttgatcattctgttcttggaggaaggagtggtatatctatctctaaactgatgacacatctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT

Basic information

species Zea mays
transcript GRMZM2G082976_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 5
aggttgcctgtatagcattctgat-tgttgccttgatcatt-ctgttcttggaggaaggagtggtatatctatctcta-aactgatga-cacatctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT
       | ||||      ||||| | ||| ||  || |    |||   |           |  |    | || |||  || |||  |  |    |  |||||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||  | ||||| |||||||| || || ||||||||||||||||
----attcggtatgaatgcctgatgtattgactgaattaaaattgtcaatatgctgttttcttcttggaccatatctgtaattgacaaatattgtttctttcagGGTATGATTGCTGGGCATGTGTACTACTTCCTGGAAGATGTATACCCGCGGATGACTGGGAGGCGTCCCCTGAAGACTCCTTCGTTCATCAAGGCGCTAT

upper sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 3'ss of exon 3
---aggttgcctgtatagcattctgattgttgccttgatcattctgttcttggaggaaggagtggtatatctatctc----taaactgatgacacatctctt-ttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT
    | ||   |  ||| || | | | |   | ||  | | || |||| |||  |       | |   |  | ||||    | |||||| |||  || | |  ||||||||||||||||||| ||||  ||||| ||||| |||||||| || || || ||||| || || || || || |  || ||    ||||| || ||  | |
gtatgttttttttcataacaatttcaattaagtctgaaac-ttgtgtt-ttgctgttgtttatagcccagttttctcatgttgaactgaagacctatttgtggttcagGGTATGATTGCTGGTCATGCCTACTATTTTCTTGAAGATGTGTATCCGCGAATGACAGGTCGTCGGCCCCTAAGAACTCCACAGTTCATTAAAGCAATGT
















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|211475995|gb|FL472681.1|FL472681
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|37379052|gb|CF626253.1|CF626253
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|37378913|gb|CF626178.1|CF626178
EST:     ATTGGGCTTCTCTAT-CTAGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: ATTGGGCTTCTCTATCCT-GGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|78543826|gb|DV621324.1|DV621324
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|166459614|gb|EG161308.1|EG161308
EST:     CTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTA
genomic: CTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTA
EST: gi|88754119|gb|DY538260.1|DY538260
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|26457330|gb|CA828913.1|CA828913
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|4573306|gb|AI586865.1|AI586865
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
EST: gi|31353782|gb|CD438139.1|CD438139
EST:     TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG
genomic: TATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGG

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: 106

GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTGgtatgcttct ... ctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggaggaaggagtggtatatctatctctaaactgatgacacatctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT
                               aactgat  putative branch site (score: 221)
                                          catctcttttc  putative PPT
                 tatatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttgcctgtatagcattctgattgttgccttgatcattctgttcttggaggaaggagtggtatatctatctctaaactgatgacacatctcttttcagGGTATGATTGCTGGACATGTGTACTACTTTCTGGAAGATGTATACCCACGGATGACTGGCCGCCGTCCGCTGAAGACACCGTCCTTCATCAAGGCGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - -gcctgta
- - - - - - - -cattctg
- - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga