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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactttttggttttgtctttggtttatatctttgtctcactctgtattagctcaatgtacatcatgtttcacgaaaacatatagtaaacaataagaagcgcttgtttgtgtagtttgaaatgtcatttactctaaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG

Basic information

species Zea mays
transcript GRMZM2G152526_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152526_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g23120.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------gtaaactttttggttttgtctttggtttatatct-ttgtctcactctgt-attagctcaatgtacatcatgttt-cacgaaaacatatagtaaacaataagaagcgcttgtt-------------tgtgtagtttgaaatgtcatttactctaaaa--tgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG
                                    |  |   ||||   |||  | |  |  || ||  ||  |  | | ||| || || | |      |  ||  |    | |   | | ||| ||| |||| | |  || | ||             ||| ||  | | ||  | ||| |   | |||  |||||||||||||||||||||| || || ||||| ||||| ||  | |||||||||||||||||||| || ||||||||||||||||| || ||| | |||||||
gtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgta-tgaatgtcggttaccagagtatgtcataagtttataagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTCAAGACGAAGAAAATATTTGTTGGTGGATTACCATCTGCTTTGAAAGAAG

upper sequence: GRMZM2G152526_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0117g00150.t01 (Vitis vinifera), 3'ss of exon 3
gtaaactttttggttttgtctttggtttatatctttgtctcactctgtattagctcaatgtacatcatgtttcacgaaaacatatagtaaacaataagaagcgcttgtttgtgtagtttgaaatgtcatttactctaaaatg---cagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG
                                            | |  | |    |||  | || |   |  ||        ||  || || ||||    |   | |||    |||||   ||| | |  | | | |||||   |||||||| ||||| ||||| || || || ||  ||| ||  | ||| |||||||| || |||||||| ||||||||||||||||| ||  |  | |  ||||
--------------------------------------------cggattaaaaataataaaaataaaaataaacttggtttcattttagaccataaatttcatat-tttactcagttt---atgacttgcattttgaaatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG
















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|6020836|gb|AW065764.1|AW065764
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|19770245|gb|BQ034966.1|BQ034966
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|22546340|gb|BU098651.1|BU098651
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|24763190|gb|CA398373.1|CA398373
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|211034282|gb|FL145439.1|FL145439
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|22472797|gb|BU037277.1|BU037277
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|211034280|gb|FL145437.1|FL145437
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|22472280|gb|BU036760.1|BU036760
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|211034286|gb|FL145443.1|FL145443
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAA
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAA
EST: gi|21760066|gb|BQ635607.1|BQ635607
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|22546609|gb|BU098920.1|BU098920
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|14569276|gb|BI097599.1|BI097599
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|22715554|gb|BU197829.1|BU197829
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|19770110|gb|BQ034831.1|BQ034831
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|211034285|gb|FL145442.1|FL145442
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
EST: gi|211034279|gb|FL145436.1|FL145436
EST:     CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCG                         GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTC

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), 49 (downstream exon)
Score: 487

CTACACACAAAAGCCCAGAGGCTTTGGCTTTATTACTTTTGCTGATCCCACTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 432

CTACACACAAAAGCCCAGAGGCTTTGGCTTTATTACTTTTGCTGATCCCACTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

CTACACACAAAAGCCCAGAGGCTTTGGCTTTATTACTTTTGCTGATCCCACTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

CTACACACAAAAGCCCAGAGGCTTTGGCTTTATTACTTTTGCTGATCCCACTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttt ... taaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaataagaagcgcttgtttgtgtagtttgaaatgtcatttactctaaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG
                                          ctctaaa  putative branch site (score: 233)
                                      tttactct  CT-rich tract
                                     atttactctaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactttttggttttgtctttggtttatatctttgtctcactctgtattagctcaatgtacatcatgtttcacgaaaacatatagtaaacaataagaagcgcttgtttgtgtagtttgaaatgtcatttactctaaaatgcagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG