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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaatgcttttggtttgggccatgaatataactacttccagtttcaaggatttcaagttcatttcttcattgaatattctttcttttactaacttatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG

Basic information

species Zea mays
transcript GRMZM2G088974_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 5
gtaatgaatgcttttggtttgggccatgaatataactacttccagtttcaaggatttcaagttcatttcttcattgaatattctttcttttactaacttatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG
             |||||      ||  ||| |   |||||  |  || |   | ||   ||   || ||| | ||     | || || | || || | ||  |  || |   ||| ||    |   |||| ||||  || || ||||| |||||||| ||||||||| ||||||||   | ||| ||| |||||||||||||||| 
------------gttggtgcttatca-aaatgttcttacttgaaactttac--acttttggtaatttccttgactg-----ttttcctatgaccaaatgatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA

upper sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgaatgcttttggtttgggccatgaatataactacttccagtttcaaggatttcaagttcatttcttcatt-gaatattctttcttttactaac--ttatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG
                          |  |||  | | |    | ||  | |||| |    |||||||   |||| |||  || ||| |  ||||     ||    ||||| |   |||  || |||   | || || |  || || |||||||||||||| ||||||||| ||||||| |||| ||| ||  |||||||||| ||| ||
-------------------------gttgatactaatgcaattatttcaatggatat----ttcatttgaacattagaagcttgtttttgatacttttgattgccctttagGTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG
















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|37375807|gb|CF624370.1|CF624370
EST:     GATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: GATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|149080861|gb|EE169941.2|EE169941
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCCATAATCCAGTTGACGCCTCATTCTTTGAA
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAA
EST: gi|76013309|gb|DT940479.1|DT940479
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTTGA-TC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTT-GAATC
EST: gi|60672399|gb|DN475149.1|DN475149
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|32928793|gb|CF033605.1|CF033605
EST:     AGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: AGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|6587603|gb|AW244921.1|AW244921
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|113702970|gb|EE680474.1|EE680474
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|101401650|gb|EB822490.1|EB822490
EST:     AGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: AGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|71766943|gb|DR964880.1|DR964880
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|93282631|gb|EB674895.1|EB674895
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|67018692|gb|CO447441.1|CO447441
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATTC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|71762698|gb|DR960635.1|DR960635
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|88753523|gb|DY537664.1|DY537664
EST:     TGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|50334940|gb|CO530066.1|CO530066
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|32929425|gb|CF034237.1|CF034237
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|89754586|gb|DY685314.1|DY685314
EST:     AAGTTGAGGCCTTAGAAGGATTTGAACCACAAAAG                         ATTAGGGTTTGTTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: AAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|50334941|gb|CO530067.1|CO530067
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|6465587|gb|AW191182.1|AW191182
EST:     CTGAGCC-CAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: CTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|93011705|gb|EB637225.1|EB637225
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|71766942|gb|DR964879.1|DR964879
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|40333919|gb|CK367989.1|CK367989
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|149080860|gb|EE169940.2|EE169940
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATTTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|71439240|gb|DR820290.1|DR820290
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|76013308|gb|DT940478.1|DT940478
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|76937581|gb|DV175190.1|DV175190
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCAACCAATA-TCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|60338966|gb|DN205939.1|DN205939
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|78075089|gb|DV503523.1|DV503523
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
EST: gi|32929559|gb|CF034371.1|CF034371
EST:     TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAG                         ATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC
genomic: TTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCC

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: 283

CAATAGCAGCTCTTTTGGGGATCGAATAGGTTCCCTCTTTTTTGCTACAATTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

CAATAGCAGCTCTTTTGGGGATCGAATAGGTTCCCTCTTTTTTGCTACAATTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

CAATAGCAGCTCTTTTGGGGATCGAATAGGTTCCCTCTTTTTTGCTACAATTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 201

CAATAGCAGCTCTTTTGGGGATCGAATAGGTTCCCTCTTTTTTGCTACAATTGGTTGTGGAGCGCAAGTTGAGGCCTTAGAAGGATCTGAGCCACAAAAGgtaatgaatg ... tatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcaagttcatttcttcattgaatattctttcttttactaacttatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG
                                     tactaac  putative branch site (score: 201)
                   attgaatattctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaatgcttttggtttgggccatgaatataactacttccagtttcaaggatttcaagttcatttcttcattgaatattctttcttttactaacttatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC