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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacgtggaacatagattcgagataacagcatttctgcatatatgtcttgttgtgacttgttgcattagttgagacttgagcgttgctactatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG

Basic information

species Zea mays
transcript GRMZM2G045366_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g54480.1 (Oryza sativa), 3'ss of exon 1
tcacgtggaacatagattcgagataacagcatttctgcatatatgtcttgttgtgacttgttgcattagt---tgagacttg-agcgttg--ctactatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG
    | || | || |||||||||||| |   ||     |||||||| |  || |   ||| |   ||| |    |||  ||| | | ||   |||| ||||||||||||||||| || ||| ||||||| ||||| |||||||||||||||||||| || |||||||||||||||| ||||
----gagggagatggattcgagataatac--ttctaatatatatgtttatttctaggttgctattttaatatgcgagtgttgtatcatttgtctaccatctggcagCCTTTGGCAGACGCATTGCATTACCAGAACCATGATGTGATCAAGATCTTGGAAAAGCATGGCTCCAAGCTTAAG
















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|74234287|gb|DT642201.1|DT642201
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|148965331|gb|EE016133.2|EE016133
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|76291780|gb|DV031348.1|DV031348
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|76288739|gb|DV028307.1|DV028307
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|211141911|gb|FL073905.1|FL073905
EST:     GCTTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCATTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATT
genomic: GCTT-CAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATT
EST: gi|71307030|gb|DR789669.1|DR789669
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|71448903|gb|DR829953.1|DR829953
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|149075835|gb|EE164377.2|EE164377
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|71441712|gb|DR822762.1|DR822762
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|148956239|gb|EC902034.2|EC902034
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|78111238|gb|DV529635.1|DV529635
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|93284065|gb|EB676329.1|EB676329
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|78080255|gb|DV508667.1|DV508667
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|76284596|gb|DV024164.1|DV024164
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|76287394|gb|DV026962.1|DV026962
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
EST: gi|76291270|gb|DV030838.1|DV030838
EST:     TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACG                         CCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT
genomic: TGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTT

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: 45 (upstream exon), 49 (downstream exon)
Score: 34

GGCGCTGCACATCGCCGCCTGCGAGGGCCACGCCGAGGTCGTCGAGCTGCTGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 61

GGCGCTGCACATCGCCGCCTGCGAGGGCCACGCCGAGGTCGTCGAGCTGCTGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG


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

GGCGCTGCACATCGCCGCCTGCGAGGGCCACGCCGAGGTCGTCGAGCTGCTGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 29

GGCGCTGCACATCGCCGCCTGCGAGGGCCACGCCGAGGTCGTCGAGCTGCTGCTTCAGAGCGGCGCGGAGGCCGCCGTGGAGGACCAGTGGGGCAGCACGgtgcggcctg ... tatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgttgtgacttgttgcattagttgagacttgagcgttgctactatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG
                   attagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacgtggaacatagattcgagataacagcatttctgcatatatgtcttgttgtgacttgttgcattagttgagacttgagcgttgctactatctggcagCCTTTGGCGGATGCAATGCATTATCAGAATCATGATGTGATCAAGATCTTTGAGAAGCATGGCTCCAAGCATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - -gaacata
- - - - - - - - - - - - aacagca
- - - - - - - - - - - - - - - - - ctgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgttgct