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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaacatgtcagtgacacatttgggattgcaaattttgcaatggcaaataactaacctctttctgcacaaaggtaactccatgttccatgtgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG

Basic information

species Zea mays
transcript GRMZM2G117507_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 5
tcaacatgtcagtgacacatttgggattgcaaattttgcaatggcaaataactaacctctttctgcacaaaggtaactccatgttccatgtgt-----atttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG
    | | |||     | |  ||       |  || | |    ||  ||   ||   | | | || ||| | || ||||  | ||||||||||      || ||||||||||||||||||||| ||||| ||||||||| | || |||||||||||||||||||||||||||||||| ||  ||||||| ||| ||||||| || 
---gcct-tcaaccttagacatgttgcaaaaggttatacctgtgcttattgttacattttatttgaacataagtgactctgt-ttccatgtgtcttcttttccagAAAATATGGTTTAAGTGACGATACTGTGGATTTCATCGGCCATGCACTTGCTCTTCATAGAGATGATCGTTACCTAAATGAACCAGCAATTGATACTGTA

upper sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 5
tcaacatgtcagtgacacatttgggattgcaaattttgcaatggcaaataactaacctc---------tttctgcacaaaggtaactc------catgttccatgtgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG
                || ||  |  || || ||  |||||  | | ||| |||  ||          |||||||| | |  ||||||      ||| | || | | | || ||||||||||||||||||||| ||||| ||||||||| | || ||||||||||||||||||||||||||||| || ||  ||||||| ||| ||||||| || 
---------------taccttcagtctttcacatgatgcaaaaggatatatctatgcttcttttaccttttctgcatataaataactctgtttccatttgccctttcttttccagAAAATATGGTTTAAGTGACGATACCGTGGATTTCATCGGTCATGCACTTGCTCTTCATAGAGATGATCGCTACCTTAATGAACCAGCAATTGATACTGTA
















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|211472425|gb|FL096495.1|FL096495
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACCACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGAATTCG
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCG
EST: gi|211472428|gb|FL096498.1|FL096498
EST:     ACATCGAGGGATTGGACCTTACTAGGGTGACCACTAGAAAAACTTATAGC                         AAAATATGGGTTTAAG
genomic: ACATCAAGG-ATTGGACCTTACTAGGGTGACAACTAGAGAA-CTTATAGCgttagtacct ... tgtatttcagAAAATATGG-TTTAAG
EST: gi|24773895|gb|CA409149.1|CA409149
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|33095042|gb|CF055036.1|CF055036
EST:     ACACGTCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|23357699|gb|BU645348.1|BU645348
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|33101772|gb|CF061732.1|CF061732
EST:     ACACATCAGGGATTGGACCTCACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|211474946|gb|FL096509.1|FL096509
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACT-ATAGC                         AAAATATGGTT-AANGTGATGATACAGTGGGATTTCGT-GGACATGCAC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAA-GTGATGATACAGTGG-ATTTCGTTGGACATGCAC
EST: gi|60396978|gb|DN229797.1|DN229797
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|18661117|gb|BM501220.1|BM501220
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|29544525|gb|CB604905.1|CB604905
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|31351669|gb|CD436026.1|CD436026
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|32943016|gb|CF047835.1|CF047835
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|32933017|gb|CF037829.1|CF037829
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|6020721|gb|AW065529.1|AW065529
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGNGGATTTCGNTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|31360108|gb|CD444465.1|CD444465
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|211472426|gb|FL096496.1|FL096496
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATANCAGTGGATTTCGTTGGACATGCACTTG
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATA-CAGTGGATTTCGTTGGACATGCACTTG
EST: gi|15313508|gb|BI478735.1|BI478735
EST:     ACACATCAAGGA-TGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|5895558|gb|AW036804.1|AW036804
EST:     CAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: CAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
EST: gi|211113229|gb|FL096514.1|FL096514
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGG
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGG
EST: gi|24773363|gb|CA408617.1|CA408617
EST:     ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGC                         AAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC
genomic: ACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGC

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), 43 (downstream exon)
Score: 347

CAAGGAACTTCTTCATTTATGTCCAAGATTACAATGAAGCTGATCCAAGGACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 573

CAAGGAACTTCTTCATTTATGTCCAAGATTACAATGAAGCTGATCCAAGGACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 536

CAAGGAACTTCTTCATTTATGTCCAAGATTACAATGAAGCTGATCCAAGGACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 214

CAAGGAACTTCTTCATTTATGTCCAAGATTACAATGAAGCTGATCCAAGGACACATCAAGGATTGGACCTTACTAGGGTGACAACTAGAGAACTTATAGCgttagtacct ... tgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataactaacctctttctgcacaaaggtaactccatgttccatgtgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG
                                             tgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaacatgtcagtgacacatttgggattgcaaattttgcaatggcaaataactaacctctttctgcacaaaggtaactccatgttccatgtgtatttcagAAAATATGGTTTAAGTGATGATACAGTGGATTTCGTTGGACATGCACTTGCTCTTCATAGAGATGATCGTTATCTCGATGAACCGGCACTTGATACAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - catgtca
- - - - - - - - acatttg
- - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - -aaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccatg