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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttattatttgttgacaaccgtgaattattgttcccatagaatggaagtcctcttatttttgtttgccagaagtaactgtgaacacatctacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC

Basic information

species Zea mays
transcript GRMZM2G071071_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071071_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 12
acttattatttgttgacaaccgtgaattattgttcccatagaatggaagtcctcttatttttgtttgccagaagtaactgtgaacacatctac---ttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC
| |   |     |||   | |    | | || |      |     | | | || ||| |  | ||| | |    ||| |   |||| |  ||     |||||||||||||||||||||||||| ||||  |||||||| || || |||| | |||||||||||||||| |||||||| |||||||| ||||||||||| | ||
attctctcaactttgcttagctc--actgttctctgtgcaactatggattacttttagtcgtcttt-ctatggttaattaacaacaaaattatgtactttcagGTGAGCCAAGACATGGGAATCGAAATGCCAATTCCTATTAGCGTGAGGTTGAGAGATTTGAACAATATTTTCTGTAGAATAGTCCATGCTGCGCAGCAGC

upper sequence: GRMZM2G071071_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 3'ss of exon 13
acttattatttgttgacaaccgtgaattattgttcccatagaatggaagtcctcttatttttgtttgccagaagtaact--gtgaacacatctacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC
   |||| | |  | |   ||   | || |  ||      ||     |   || |   || | ||     |   ||| |   | ||  ||| ||||| | |||||||||| ||||||||||| |||||||||||||| || ||||| | | |||| ||||||||||| ||||||||| | ||||| ||||| ||||| | ||
caatattgtctact-attgccaccagttttctttatgtctgatctctacagctatggattattttcagttgttttaattcaataaaatcatgtacttgt-agGTGAGCCATGACATGGGAATCGAAACACCAATTCCTATTAGTGTAAGGTTGAGGGATTTGAACAATATTTTCTGCCGGATAGTCCATGCGGCGCAGCAGC
















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|31359528|gb|CD443885.1|CD443885
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|67019644|gb|CO448393.1|CO448393
EST:     CGAAAGA-GATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32841088|gb|CD980769.1|CD980769
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|148933976|gb|EC877974.2|EC877974
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|67017730|gb|CO446479.1|CO446479
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGNGGAATTGAAACACCAATTCCGATCAGTGTGAAGCT
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATG-GGAATTGAAACACCAATTCCGATCAGTGTGAAGCT
EST: gi|32840501|gb|CD980182.1|CD980182
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|71443064|gb|DR824114.1|DR824114
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|60345129|gb|DN212102.1|DN212102
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32840298|gb|CD979979.1|CD979979
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|31356495|gb|CD440852.1|CD440852
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|31357304|gb|CD441661.1|CD441661
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32840287|gb|CD979968.1|CD979968
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32839739|gb|CD979420.1|CD979420
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|87152121|gb|DY396910.1|DY396910
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32839495|gb|CD979176.1|CD979176
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|18385253|gb|BM418452.1|BM418452
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATNGAAACACCAATTCCGATCAGNGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32839754|gb|CD979435.1|CD979435
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|60350823|gb|DN217796.1|DN217796
EST:     AGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: AGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32933393|gb|CF038205.1|CF038205
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|76011272|gb|DT938442.1|DT938442
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|37379192|gb|CF626328.1|CF626328
EST:     CCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
EST: gi|32840274|gb|CD979955.1|CD979955
EST:     CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGA                         GTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG
genomic: CGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTG

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: 244

TACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCTGCGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

TACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCTGCGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

TACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCTGCGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 233

TACACATGGAGAAAATACTGGCTACGAAGTTCCGTGCTTGATAGTTGCTGCGAAAGATGATCTTGACCAATCTTCACAAGCTCTACAAGAATCAACTAGAgtaagttttt ... tacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtcctcttatttttgtttgccagaagtaactgtgaacacatctacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC
                          aagtaac  putative branch site (score: 233)
                                           tctacttttc  putative PPT
       tcttatttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttattatttgttgacaaccgtgaattattgttcccatagaatggaagtcctcttatttttgtttgccagaagtaactgtgaacacatctacttttcagGTGAGCCAAGACATGGGAATTGAAACACCAATTCCGATCAGTGTGAAGCTGAGAGATTTGAACAACATTTTCTGCAGAATAGTACATGCTGCGCAACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaca