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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaaaggcttgctcgtagtctatgcgttgtgttgttggacaaaagttaatataaaccattttttgtgttgaataactctaatggctaataacaaacgatgaattttgcataatttattatgttttgactacttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 3
gtatgccaaaggcttgctcgtagtctatgcgttgtgttgttggacaaaagttaatataaaccattttttgtgttgaataactctaatggctaataacaaacgatgaattttgcataatttattatgttttgactacttttgtt----cagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG
                                                   |  | ||   |||    |  |  | ||  || |  |  |   |   |         |||| ||   || ||| | ||| |  |  || ||||    ||||||||||||||||||||||||| ||| |||| ||| | |||||||| || ||||| ||||||||||||
--------------------------------------------------attttctatctcatcaccttggaggcatttctgttttcacatttgcaattttcctggttttacaaggttcattgtatttgggttctttctgtttttgcagGTATTGTGGTTACTAATGATGGCAATGCTATATTGCGAGAAATAGATATTGCACATCCTGCTGCCAAG

upper sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 3
gtatgccaaaggcttgctcgtagtctatgcgttgtgttgttggacaaa-agttaatataaaccattttttgtgttgaataactctaatggctaataacaaacgatgaattttgcataatttattatgttttgactacttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG
                               || | |||   | |||| | || |||  ||  | | ||    ||    ||  | | |  || |          | |||||    | || ||||   || ||  | || |    ||||||||||||| ||||||||||| ||||||||| |  ||||  ||||  | || || || ||||| |||
-----------------------------tattttcttgactgccaaacattttataataataaatcttaccttttgtcaagcccagttactta---------gtcaatttc---tgatctattt--ttctggatgctgt----cagGTATTGTGGTCACTAATGATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG
















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|71438455|gb|DR819505.1|DR819505
EST:     ACATTGGGTCCCAGATCCATGCTGAAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: ACATTGGGTCCCAGATCCATGCTG-AAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|211175329|gb|FL101110.1|FL101110
EST:     CACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|211175332|gb|FL101113.1|FL101113
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|211175327|gb|FL101108.1|FL101108
EST:     CACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|71332448|gb|DR803183.1|DR803183
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|31354620|gb|CD438977.1|CD438977
EST:     CACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|211175325|gb|FL101106.1|FL101106
EST:     CACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|211175333|gb|FL101114.1|FL101114
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|71428865|gb|DR809915.1|DR809915
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|94478012|gb|EB706970.1|EB706970
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|71448421|gb|DR829471.1|DR829471
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|211175328|gb|FL101109.1|FL101109
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|30306946|gb|CD001619.1|CD001619
EST:     GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
EST: gi|74244741|gb|DT652655.1|DT652655
EST:     GACATTGGGTCCCAGATCCATGCTGAAAACGCTTCTGGACGCTGGTGGAG                         GTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG
genomic: GACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCG

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: 473

GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

GCTGTTGCTGACATCATTCGCACGACATTGGGTCCCAGATCCATGCTGAAAATGCTTCTGGACGCTGGTGGAGgtatgccaaa ... ttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataacaaacgatgaattttgcataatttattatgttttgactacttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG
                                            cttttgttc  CT-rich tract
           atgaattttgcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaaaggcttgctcgtagtctatgcgttgtgttgttggacaaaagttaatataaaccattttttgtgttgaataactctaatggctaataacaaacgatgaattttgcataatttattatgttttgactacttttgttcagGTATTGTGGTTACTAATGATGGTAATTCTATTTTGAGGGAAATAGACATCGCACACCCTGCTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC