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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttcattgagttcacatcagtatcttatttgactattgtacatgacattgttatattgcagttgtgctagtaaggttggttttggtgaatacttg...

Basic information

species Zea mays
transcript GRMZM2G104632_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104632_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 5'ss of exon 6
AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttcattgagttcacatcagtatct-tatttgactattgtacatgacattgttatattgcagttgtgctagtaaggttggttttggtgaatacttg----
||||||| ||||||||||| || |||||||| || |||   || ||||||||||||||||| ||||||||||| ||||| |||||||| || |||||||||||||    ||  ||| ||| |  | |    ||  ||| ||      ||| ||   |||| |||   |     || |  | ||| |  |  | | ||        
AGTATGACTCCACTCATGGTCCATTTAAAGGCTCCATTAAGGTTGTGGATGATTCAACCCTGGAGATCAATGGAAAGAAAGTCACAATCACTAGCAAAAGgtaat----atcaagtccacttagggactagtacatgattacatagaatgtcacaattat-ttgttatctaagtattgtgtttgatgattattagtaaaaaaaaa
















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|60397796|gb|DN230612.1|DN230612
EST:     ATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: ATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|9961539|gb|BE644327.1|BE644327
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAAT
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAAT
EST: gi|67017162|gb|CO445911.1|CO445911
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|211009063|gb|FL066254.1|FL066254
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|21088933|gb|BQ401246.1|BQ401246
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|6564069|gb|AW231691.1|AW231691
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|28987666|gb|CB351748.1|CB351748
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|166438613|gb|EG185317.1|EG185317
EST:     ATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: ATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|24769367|gb|CA404496.1|CA404496
EST:     AATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: AATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|5928870|gb|AW056162.1|AW056162
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|21809653|gb|BQ667971.1|BQ667971
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
EST: gi|91869745|gb|EB400519.1|EB400519
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCCATGGGGTAACTTTGGGGCTGAATATGTTGTTG
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCC-ATGGGGTAACTTTGGGGCTGAATATGTTGTTG
EST: gi|211011829|gb|FL066255.1|FL066255
EST:     GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAG                         AGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA
genomic: GATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGA

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: 848

AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 353

AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 394

AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1183

AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttca ... tatattccagAGATCCTGCAGAGATTCCATGGGGTAACTTTGGGGCTGAATATGTTGTTGAATCTTCTGGTGTCTTCACGACGACTGATAAAGCATCAGCACACTTAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATGATTCCACTCATGGCCCGTTTAAAGGTTCTATTCGTGTCGTGGATGATTCAACCCTCGAGATCAATGGGAAGAAGGTCACAATTACAAGCAAAAGgtaatgttcattgagttcacatcagtatcttatttgactattgtacatgacattgttatattgcagttgtgctagtaaggttggttttggtgaatacttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA