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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagcacgtcgcctagtctataaatgtgaattgcctctttgcttacgtgcacaatcttaccattggttttcttacattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG

Basic information

species Zea mays
transcript GRMZM2G465169_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G465169_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 5
---------gtaaaag--cacgtcgcctagtctataaatgtgaattgcctct-ttgcttacgtgcacaatctta-ccattggttttcttac-attcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG
         |||| |     | ||        | |     |||| |    ||  |  || | || |||||   | | | ||| || |||    ||| ||||||||||| || |||||||| ||||| |||||||||||||||||||||||||||| | |||||||| |||||||||||||||| ||||||||||||||||
ttgattcttgtaatatgtttcatcattgttcttgtcttattgaaatatgactactctttgcatggacaatagcatctaatggcttgcttcttgttctcagCTTCAAGAGCTTGCTGGTCAACTCTACGATCTTTGGGATCTCATGGATGCCCCCATGCAAGAAAGGAGCATGTTTGATCATGTCACCTGCAACAGATCAG
















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|33095065|gb|CF055059.1|CF055059
EST:     ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
EST: gi|32846311|gb|CD985992.1|CD985992
EST:     ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
EST: gi|32848300|gb|CD987981.1|CD987981
EST:     ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
EST: gi|32944328|gb|CF049147.1|CF049147
EST:     ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
EST: gi|32930378|gb|CF035190.1|CF035190
EST:     ACAGGACGGTAGCTACACTTAATGAAGATAAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTCAGCTCTACGATCTTTGGGATCTCATGGATGCC
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCC
EST: gi|211094979|gb|FL279271.1|FL279271
EST:     ACAAGACGGTAGCTACACTTAATGAAGATNAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATG
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATG
EST: gi|211094978|gb|FL279270.1|FL279270
EST:     ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGCTGCGTCTAAGCAAG                         CTTCAAGAACTCGCTGGTC
genomic: ACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTC

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: 657

TGTTGGCGACAACTGTAAGAGCATTAGTGATGATACATTATCAAAACTTGACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 100

TGTTGGCGACAACTGTAAGAGCATTAGTGATGATACATTATCAAAACTTGACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 65

TGTTGGCGACAACTGTAAGAGCATTAGTGATGATACATTATCAAAACTTGACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 107

TGTTGGCGACAACTGTAAGAGCATTAGTGATGATACATTATCAAAACTTGACAAGACGGTAGCTACACTTAATGAAGATAAGAAGTTGCGTCTAAGCAAGgtaaaagcac ... acattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgcctctttgcttacgtgcacaatcttaccattggttttcttacattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG
                                        ttcttac  putative branch site (score: 107)
                                      ttttcttac  CT-rich tract
                                      ttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagcacgtcgcctagtctataaatgtgaattgcctctttgcttacgtgcacaatcttaccattggttttcttacattcacagCTTCAAGAACTCGCTGGTCAGCTCTATGATCTTTGGGATCTCATGGATGCCCCCAAGGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA