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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagaatgtcccactcaaatagtttagcagattttgaaattgaaaatactatattgtagcatttttgttgaatattgatgtattgcctcttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA

Basic information

species Zea mays
transcript GRMZM2G138505_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 10
tgaagaatgtcc-cactcaaatagtttagcagattttgaaattgaaaatactatattgtagcatttttgttgaatattgatgtat---tgcctcttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA
|   || ||||  ||  |||     | |    ||||   || | |||| |    | ||||||   |   |  ||||||||| | |   |   ||   |||||||||||||||||||  ||| || ||||||||||| |||||||| ||||| ||||| ||||||||||||||||||||||||||| || | |||||||| ||||
ttttgagtgtctgcatgcaacgcagtcaaggaattt---aact-aaaacatagaaatgtagctcctacatgtaatattgatatgtacatttatcactatcgcagAAAGTTGTGACAATGACACCCTGTATGTGGAACGGAACAAAGAGACCATGCTACCTTTTTGCTAGAAAGTTTTACCCAGAAGCTCTCAACAACCTACTGA
















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|9254423|gb|BE344891.1|BE344891
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|78081339|gb|DV509751.1|DV509751
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|211360336|gb|FL143959.1|FL143959
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|32864122|gb|CF003804.1|CF003804
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|101387921|gb|EB815974.1|EB815974
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|71762140|gb|DR960077.1|DR960077
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|211360335|gb|FL143958.1|FL143958
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
EST: gi|71772236|gb|DR970173.1|DR970173
EST:     TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAA                         AAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC
genomic: TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGC

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: 45 (upstream exon), 47 (downstream exon)
Score: 117

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 100

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 107

TCTGTCAATGAGAATGTTCACATTACAAGTGATGATAAAgtaagcatat ... ttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatactatattgtagcatttttgttgaatattgatgtattgcctcttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA
                            tattgat  putative branch site (score: 107)
                                      ttgcctcttc  putative PPT
                atttttgttgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagaatgtcccactcaaatagtttagcagattttgaaattgaaaatactatattgtagcatttttgttgaatattgatgtattgcctcttcatcgcagAAAGTTGTGACACAGACCCCATGTATGTGGAATGGAACAAAAAGACCCTGCTATCTTTTTGCTAGAAAGTTTTACCCAGAATCTTTGAACAACCTGCTGA

- - - - - -ccactca
- - - - - - - - - - - - - - - - - - - - - gaaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta