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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataagatattcaaaaaatcattggggtcagttgaccccaaaataagggctagctccgcccctgataccagccatgtgaaccaaacctttgctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG

Basic information

species Zea mays
transcript GRMZM2G004572_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os10g25090.1 (Oryza sativa), 3'ss of exon 15
-tataagatattcaaaaaatcattggggtcagttgaccccaaaataagggctagctccgcccctgataccagccatgtgaaccaaa-cctttgctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG
|||| | |||| | ||| | || | | | || | || ||| | || ||||||| |||| || | ||||||||||| ||||||||||| || |||||||||||||||||||||||||| || || |||||||||||||||||||| ||||||||| | || ||||| |
gtatataaccttcactcctggtacaatgcagtttgccagcatattcataactgaa--caccaaggatctgaattataccaaccaaaaccttcactatttcagCCTGAGCCGGAGTTCAGACCGCCGATGTCTGAGGTGGTGCAAGCGCTGGTCCGCCTTGTTCAGAGGGCCAACATGACTAGGAGAATGATCGACGGCGAAG

upper sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
tataagatattcaaaaaatcattggggtcagttgaccccaaaataagggctagctccgcccctgataccagccatgtgaaccaaacctttg--ctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG
| ||| | | | | | || | ||| | | | |||| | | ||| ||| | ||||| ||||||||||| ||||| || |||||||| ||||||||||| |||| | || ||||| || ||||||| || ||||| | | | ||
-----------------------gtaatcatctatatattataatgtgatgatctgaacaaatgaaatctga-atgtatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT

upper sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 15
tataagatattcaaa-aaatcattggggtcagttgaccccaaaataagggct-agctcc--gcccctgataccagccatgtgaaccaaacctttgctggt-----gcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG
|||| | || | ||| | | | ||| || || || | | |||| | | | | | | ||| || ||| | || ||||||||||||||||||| | || |||||||| || ||||||||||| ||||||||||| || ||| |||| ||||||| || ||||| | | |||
-gtaaggtgtttagttaaagtaaagagtgcagatggattcatcatcctgtttcagctgctgatggtaaagatctgttctctgattttaatattttatcgttttgggcagCCTGAGCCAGAGTTCCGGCCACCAATGTCAGAAGTGGTGCAAGCACTGGTGCGGCTAGTCCAGCGGGCAAACATGAGCAAGAGAACCATTAGTAACGAAC

upper sequence: GRMZM2G004572_T01 (Zea mays), 3'ss of exon 15
lower sequence: PP1S242_37V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------------tataagatattcaaaaaatcattggggtcagttgaccccaaaataagggctagctccgcccctgatacc---agccatgtgaaccaaacctttgctggt---------------gcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG
|||| || ||| | | | | | | || | | || | | | | | | |||| ||| || | | | |||| ||||||||| || || ||| ||||||| |||||||| ||||| ||| ||||||| || ||| | ||| | |||| ||| || | | | | | |
gtgcgtcacttacgaattccctctttgctgttccatgaatttctcatctatgaatcataacttactcacatctgccatagaacttaccatctcttccatcaatacaagattgtcattcggtctcccaatccatctgactcatgcgctggttggttttatatttttgggtgcagCCTGAACCCGAATTCCGACCTCCCATGTCTGAAGTGGTACAATCGCTGGTACGCCTCATGCAGCGCGCCACGCTGAGCATCAAGCGCCGATCCAGTGGAG

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|211231141|gb|FL457454.1|FL457454
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|93281943|gb|EB674207.1|EB674207
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|211297738|gb|FL108113.1|FL108113
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|76014323|gb|DT941493.1|DT941493
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|113641288|gb|DW804432.1|DW804432
EST:     CGCCAAATACCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGG
genomic: CGCCAAAT-CCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGG
EST: gi|18180795|gb|BM382005.1|BM382005
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|93281944|gb|EB674208.1|EB674208
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|74241624|gb|DT649538.1|DT649538
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTTTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|211231140|gb|FL457453.1|FL457453
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
EST: gi|76018776|gb|DT945946.1|DT945946
EST:     CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAG                         CCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG
genomic: CCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTG

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: 78

CATTGACGCCTTGGACCAGATGGTTGATCCGGCGCTCAAGGGTCTTTACCCCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 21

CATTGACGCCTTGGACCAGATGGTTGATCCGGCGCTCAAGGGTCTTTACCCCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 17

CATTGACGCCTTGGACCAGATGGTTGATCCGGCGCTCAAGGGTCTTTACCCCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

CATTGACGCCTTGGACCAGATGGTTGATCCGGCGCTCAAGGGTCTTTACCCCGCCAAATCCCTTTCCCGTTTTGCGGATGTTATTGCTCTGTGTGTCCAGgtatgaactc ... gctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggctagctccgcccctgataccagccatgtgaaccaaacctttgctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG
              ccctgat  putative branch site (score: 191)
 cctttgct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataagatattcaaaaaatcattggggtcagttgaccccaaaataagggctagctccgcccctgataccagccatgtgaaccaaacctttgctggtgcagCCTGAGCCAGAGTTCAGACCTCCAATGTCTGAGGTGGTGCAAGCGCTGGTGCGGCTCGTTCAGAGGGCCAACATGACCAGGAGAATGCTAGATGGCGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaa