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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactactgatttcattctcttttttttttgttattacgatgggtagtgtgctgcaatttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG

Basic information

species Zea mays
transcript GRMZM2G020574_T08
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g45350.2 (Oryza sativa), 3'ss of exon 3
gtaactactgatttcattctcttttttttttgttattacgatgggtagtgtgctgcaatttgtatcttatttttatttctgcttga--actttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
||| ||| || || ||||       |||  | || ||    |      | ||  ||||    |||| ||     | || | ||| |  | |||| | | ||||||||| ||||||||||| |||||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||| ||||||||||| |||
gtatctattggttccatttctacggtttccttttcttttagt------tttgtggcaagc-atatcctagc---aattttacttaaccattttcctctggtagGCAGAACAACACTTCCTAAAGCACAACGATGCTGGATCATGGATTCAAGATTCCGCTGTGATGCTTTCTGTTAGCAAAGAAGTTCCATGGTACCTG

upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G16860.1 (Glycine max), 3'ss of exon 3
gtaactactgatttcattctcttttttttttgttattacgatg--ggtagtgtgctgcaat--ttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
|||  ||   ||       |  | | ||  | |||| | ||    | |  ||| ||   |   ||||   | || || |       || |   || |  || |||||||||||||| || || || ||||||||||| || |||||||| |||||||| ||  ||||||| ||  | || ||||||||||| |||||||||
gtatgtagacataaagcattaatatcttcattttataaggacattgcttatgtcctcttaccgttgtgattaatattgaacctgtttttacaattttccttttagGCAGAGCAACATTTTCTTAAACACAATGATGCTGGTTCCTGGATACAAGATTCTGCTTTGATGCTATCAATGAGTAAAGAGGTTCCTTGGTATCTG

upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G02920.1 (Glycine max), 3'ss of exon 3
gtaactactgatttcattctcttttttttttgttattacgatg--ggtagtgtgctgcaat--ttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
|||  ||   ||      ||  | | |   | |||  | ||||  | |  |||  |   |   ||||   | || || |        |  | |||   ||| |||||||||||||| || || || ||||||||||| || |||||||| |||||||| ||  ||||||| ||  | || ||||||||||| |||||||||
gtacgtagacataaagcactaatatctccattttacgaggatgttgcttatgtcatcttaccgttgtgattaatattgaacctcatctataattttccttt-tagGCAGAGCAACATTTTCTTAAACACAATGATGCTGGTTCCTGGATACAAGATTCCGCTTTGATGCTATCAATGAGTAAAGAGGTTCCTTGGTATCTG

upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 3'ss of exon 3
gtaactactgatttcattctcttttttttttgttattacg-atgggtagtgtgctgcaatttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
|||  ||   ||||  || | |||| ||||| ||||| |  ||  |   | |  |||| ||  | |  || ||   ||  ||        |   || |  ||||||||||||| || ||||| ||||||||||| || || ||||| |||||||||||  ||||| | ||  | || || |||||||| |||||  ||
gtacttagatattttgttttattttattttt-ttattgcacatttgatttatattgcagttgtttttctagttggtttgatgacattctctatcttgttcagGCAGAGCAACATTTTCTGAAACACAATGATGCTGGTTCGTGGATACAAGATTCGGCTTTGATGTTGTCCATGAGTAAGGAGGTTCCCTGGTACTTG

upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ13632 (Selaginella moellendorffii), 3'ss of exon 3
gtaactactgatttcattctcttttttttttgttattacgatgggtagtgtgctgcaatttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
        || |   ||| |  || |||||  ||  | |  ||| | | || | | |    | ||      |   |   ||| |              ||||||||||| || ||  |||||||||||||  |||| |||||||||||||| |||||  | ||||||||    | ||| |||||||| ||||   ||
---gtgggtgctccgattttaattctttttactt--tcccgtggatcg-gttcagaa----gcattgagagtgcgtcgttgcat--------------tagGCAGAGCAGCATTTTTTGAAGCACAATGACACCGGCTCCTGGATTCAAGACTCGGCTCTCATGCTTTCAAACAACAAGGAGGTTCCTTGGTTCTTG

upper sequence: GRMZM2G020574_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ28927 (Selaginella moellendorffii), 3'ss of exon 3
gtaactactgatttcattctcttttttttttgttattacgat--gggtagtgtgctgcaatttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
                             | | |  | ||||     |  | | ||      || |||   |    |    ||   |  | |  ||    ||||||||||| || ||  |||||||||||||  |||| |||||||||||||| |||||  | ||||||||    | ||| |||||||| ||||   ||
----------------------------gtgggtgctccgatttaattcttttactttcccgtggatcggttcagaagcattgagagtgcgtcgttgcattagGCAGAGCAGCATTTTTTGAAGCACAATGACACCGGCTCCTGGATTCAAGACTCGGCTCTCATGCTTTCAAACAACAAGGAGGTTCCTTGGTTCTTG

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|78120512|gb|DV538896.1|DV538896
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|149082587|gb|EE171783.2|EE171783
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|71764333|gb|DR962270.1|DR962270
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|78112887|gb|DV531281.1|DV531281
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|71448689|gb|DR829739.1|DR829739
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|149076432|gb|EE165055.2|EE165055
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|71447086|gb|DR828136.1|DR828136
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|149088920|gb|EE178061.2|EE178061
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|89764186|gb|DY691084.1|DY691084
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|148956593|gb|EC902440.2|EC902440
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|149102431|gb|EE287794.2|EE287794
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|149031458|gb|EE286351.2|EE286351
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGTCGGATCCTGGATTCGAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
EST: gi|78091038|gb|DV519412.1|DV519412
EST:     CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACG                         GCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT
genomic: CACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGAT

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: 44 (upstream exon), 48 (downstream exon)
Score: 177

GGTCCTACCACTTGTAGTTGCCATCTCTGGGAGAGTTGGTTCAGACACACCACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 129

GGTCCTACCACTTGTAGTTGCCATCTCTGGGAGAGTTGGTTCAGACACACCACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 210

GGTCCTACCACTTGTAGTTGCCATCTCTGGGAGAGTTGGTTCAGACACACCACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 159

GGTCCTACCACTTGTAGTTGCCATCTCTGGGAGAGTTGGTTCAGACACACCACTTATATGCCAACAAAGCGGCATGAGAGGTGTAATTGTTGAAGAAACGgtaactactg ... ctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtgctgcaatttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG
                                         ctttctttttgt  CT-rich tract
          aatttgtatcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactactgatttcattctcttttttttttgttattacgatgggtagtgtgctgcaatttgtatcttatttttatttctgcttgaactttctttttgtagGCAGAGCAACACTTCCTGAAGCACAATGATGCCGGATCCTGGATTCAAGATTCGGCAGTGATGCTTTCTGTTAGCAAAGAGGTTCCATGGTATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG