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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattctttatctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA

Basic information

species Zea mays
transcript GRMZM2G095969_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
-tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattctttatctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA
  ||  || || |||   |||   | | ||| |  |   | | || |  |  || |     | |  |||   |  || |      | |       | |||||| ||||||| ||||||||||| ||||  ||||||||||||||||||| ||| |||||||  |||||| |||||||||| ||||| |||||||| |||||
aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtacaat-gcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 7
tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattcttta--tctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA-----------------------
                         | ||| |  |   ||    | ||  ||||  || |  | |  |||   |  || |      | |        |||| || ||||||| ||||||||||| ||||  |||||| | |||||||||| ||| |||||||  |||||  |||||||||| ||||| |||||||| |||||                       
------------------------tagcaattaaaacgttct-cattccattataattcagttatgtcaggtaaaccatactgacttaatgtaccaatgcatgtattaatggatgctctctgaagACTAGTGAAAATTTCGAGGTTCTACAAGGTATTCCTGCAGAGAGAATGATGATAGAGACAGACTCTCCATACTGTGATATTAAAAATACTCATGCTGGAA

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 9
-----tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattctttatctcccagtcgagtcagatgattgtgaatcgtggttg-cagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA
     ||||   |||| | ||| |  ||        | ||  | ||   |||  | | |    |   ||  | |    |  | |  || |   | ||       |||||| ||||||||||||||||| |||   ||||||||||| ||| || | || |||||||| |||||  ||||||| || ||||||||||||||||||||
ataattttctgcttggtttttgttttcttg------tatatgacttttcacttagatgtcagatgaatcttaataatctttgttcttttttctttgtacccaatagGTGTAAATGGTTGCTCTCTGAAGACTGCTGAAAATCTTGAAGTTGTAAGGGGTATTCCTGTTGAGAGACTGATGATTGAGACAGATTCTCCATATTGTGA

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|60340099|gb|DN207072.1|DN207072
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|101392457|gb|EB818158.1|EB818158
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|88757501|gb|DY541642.1|DY541642
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|78179334|gb|DV549707.1|DV549707
EST:     CTCAGCAGAAGATCGGGACAGGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|71774366|gb|DR972244.1|DR972244
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|149089637|gb|EE178891.2|EE178891
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|76021691|gb|DT948861.1|DT948861
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|74242558|gb|DT650472.1|DT650472
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACAAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|7009462|gb|AW455727.1|AW455727
EST:     CTCAGCAGAAGATCGGGACAGGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGCTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|94477631|gb|EB706589.1|EB706589
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|71325561|gb|DR799471.1|DR799471
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGNAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|76936926|gb|DV174965.1|DV174965
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|211484453|gb|FL145754.1|FL145754
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGTTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|60341449|gb|DN208422.1|DN208422
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|78074889|gb|DV503323.1|DV503323
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|76021692|gb|DT948862.1|DT948862
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|78108903|gb|DV527320.1|DV527320
EST:     TCAGCAGAAGATCGGGACATGCTACTTTCTTTTTGAGAAGATGTTTATAG                         GTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
genomic: TCAGCAGAAGATCGGGACATGCTACTTTCTTTT-GAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG
EST: gi|13382254|gb|BG458929.1|BG458929
EST:     CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG                         GTGTTAATGGGTGCTCTCTGAAAACTAACGAAAATCTTGAGGGTCTACGAG
genomic: CTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAG

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: 44 (upstream exon), 49 (downstream exon)
Score: 83

ATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 51

ATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 80

ATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 38

ATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAGgtaaaatctc ... gtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgttattctttatctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA
     ttattctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattctttatctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- -ccatttg
- - - - - - - - - - - - -aacaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgattg