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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT

Basic information

species Zea mays
transcript GRMZM5G822591_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
gtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT
                        | |||  |   || || ||    ||||| |     | |      | |     |||   |  || |  | || |||||||||| || || ||  |  |||  ||||   ||||| |||||||||||||||||||| || ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||| |||||||||||||
----------------------caattgaagt---gaaacaagc---aagctcacctgattttttttatta---tttag---gcataatctgtattgcattctgatgagtaa-catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 27
gtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT
                                 |   ||   |  | |||| |  |||    |     ||   |  |  |  |  || |  | || |||||||||| || || ||  |  |||  ||||   ||||| |||||||||||||||||||| || ||||| ||||| || ||| |||||||  ||||||| ||||||||||||||||||||||| |||||||||||||
---------------------------------aattgaagtgaaacaagcaagctcacctgattttttattattatt-taggcataatctgtattgcattctgatgagtaa-catctataattgtgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT
















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|211415580|gb|FL028984.1|FL028984
EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAG                         GGTAAGARAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC
EST: gi|166461461|gb|EG159431.1|EG159431
EST:     ATTTCATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: ATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC
EST: gi|60399410|gb|DN232222.1|DN232222
EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC
EST: gi|67014450|gb|CO443199.1|CO443199
EST:     CTGGTGACCGTGAACTGTCAGAAGACTTGCTTGTCTATTTCATCGAGCAG                         GGGTA-GAAAGAATGCNNTTGCTTC-TGCCTCTTCATTTGCTACGAC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGG-TAAGAAAGAATGCT-TTGCTTCCTGCCTCTTCATTTGCTACGAC
EST: gi|60395619|gb|DN228489.1|DN228489
EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC
EST: gi|67016082|gb|CO444831.1|CO444831
EST:     CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAG                         GGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATC

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: 163

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 166

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttca ... tgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT
                                            atgtaac  putative branch site (score: 182)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCCTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA