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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttgacgtttaaacgtcgtttaaacatagttttaataacactggatattacttgccaattgatggtaataatttgagtctgtatccttgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 3'ss of exon 3
-------atttttgacgtttaaacgtcgtttaa-------acatagttttaataacactggatattacttgccaattgatggtaataatttgagtctgtatccttgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG
       | | |   | |||   |||||  |          | | | |   | | | |||| | ||  | |   | | ||  |  | ||| |    ||||   || |||  ||||||||| ||| |||||||||||||||| ||||| || |||||||| || ||| | |||||||| |||   |||||||  |||
gtaatggaatgtgtgcatttgtgcgtcgactggtgcaagcgcgtggctagtagagcgctgggtgtttttaggggagt-atact--tgattcgg---tgtaattttctgtgctagGAACAATGAGGTTCAGTTTGCTGGACAGCTCCAGCCGAAGGGATGTTGTTACCGTTTGGAGGTCCCGCGCGGGCAGAACGAG
















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|149027382|gb|EE046514.2|EE046514
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|88755472|gb|DY539613.1|DY539613
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|149058050|gb|EE156735.2|EE156735
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|87152120|gb|DY396909.1|DY396909
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|211353775|gb|FL303049.1|FL303049
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|18450704|gb|BM428982.1|BM428982
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|78022867|gb|DV491254.1|DV491254
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
EST: gi|148996196|gb|EE035468.2|EE035468
EST:     GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAG                         GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA
genomic: GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTA

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: 310

GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 206

GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 160

GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG


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

GTGGTTCTGATGGCCTTCGAGTGCCCACATTGTGGTGAGAGgtaacgatat ... tgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatattacttgccaattgatggtaataatttgagtctgtatccttgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG
              aattgat  putative branch site (score: 159)
                                       tatcctt  putative PPT
                       taataatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttgacgtttaaacgtcgtttaaacatagttttaataacactggatattacttgccaattgatggtaataatttgagtctgtatccttgtgttgtagGAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - aaacata
- - - - - - - - - - - - - - - - - - aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatc