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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagcatgctaagtgtgccattagtaagtggtgaatgtttttcatttattctcgttctttgtacatcttatttgaatttccatactgcctatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG

Basic information

species Zea mays
transcript GRMZM2G097995_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097995_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G07120.2 (Glycine max), 3'ss of exon 3
tgtagcatgctaagtgtgccat-tagtaagtggtgaatgttttt-catttattctcgttctttgtacatcttatttgaatttccatactgcctatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG
| |  | || |  |  |    | ||| |  |        || || ||||| ||    ||  ||| | ||||       |||    || |||    | | |||||||| | |||||||||||||  |||| |||||||||||||| || ||  |   |   ||      ||||   | ||||||| |   | ||
ttttccttgatctgcatctattctagaatatttctttcattcttgcattttttacattttcttgcatatctccagctgattat--tattgcaatgtatgcagGTCTTCTTCTCTGGAACCAGATGAGACGACAGTGGGTTGGAAACAGAAGGCATGAGAATAAGA---AACAAGTTGGAGAACCTATAATAAG
















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|4887380|gb|AI677479.1|AI677479
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGG
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGG
EST: gi|6431871|gb|AW172075.1|AW172075
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|32165086|gb|CD670404.1|CD670404
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|211490460|gb|FL154418.1|FL154418
EST:     TCAGCATGCGTCAGGAAGTTGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|28910854|gb|CB331648.1|CB331648
EST:     TCAGCATNCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|211525931|gb|FL453813.1|FL453813
EST:     TCAGCATGCGTCAGGAAGTTGCASCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGYTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|22472576|gb|BU037056.1|BU037056
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTTTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|26558641|gb|CA830876.1|CA830876
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|87156696|gb|DY401485.1|DY401485
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|31664502|gb|CD573435.1|CD573435
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|18171092|gb|BM340932.1|BM340932
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|29130220|gb|CB380924.1|CB380924
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|87155503|gb|DY400292.1|DY400292
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|28909927|gb|CB331169.1|CB331169
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|31664503|gb|CD573436.1|CD573436
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|29543916|gb|CB604296.1|CB604296
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|211490454|gb|FL154412.1|FL154412
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAAC
EST: gi|211490455|gb|FL154413.1|FL154413
EST:     TCAGCATGCGTCAGGAAGTTGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|29543917|gb|CB604297.1|CB604297
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|31909751|gb|CD651076.1|CD651076
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|21987228|gb|BQ778756.1|BQ778756
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|22472577|gb|BU037057.1|BU037057
EST:     TCAGCATGCGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
EST: gi|29544694|gb|CB605074.1|CB605074
EST:     TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAG                         GTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC
genomic: TCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAAC

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: 116

CAATCGCAGAGGAGCATGTCTTCGATCAGCACGTTGGCTCAGTCCAGCGATCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 77

CAATCGCAGAGGAGCATGTCTTCGATCAGCACGTTGGCTCAGTCCAGCGATCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

CAATCGCAGAGGAGCATGTCTTCGATCAGCACGTTGGCTCAGTCCAGCGATCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

CAATCGCAGAGGAGCATGTCTTCGATCAGCACGTTGGCTCAGTCCAGCGATCAGCATACGGCAGGAAGTAGCAGCAACCCGAATGAGTTTATGAATCAAGgtgaattcat ... tatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattctcgttctttgtacatcttatttgaatttccatactgcctatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG
                                           cctatttttc  CT-rich tract
                    atcttatttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagcatgctaagtgtgccattagtaagtggtgaatgtttttcatttattctcgttctttgtacatcttatttgaatttccatactgcctatttttcagGTCTTATGCTCTGGAACCAGACCAGACAACAGTGGGTTGGAAGCAAAAAACGCCACTCTAGATCTCAACAGCCTCGAGAACCAAAGTTGAG

- -agcatgc
- - - - - - - - tgccatt
- - - - - - - - - - - - - - - -gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgcc