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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcgacccttccgcgtctcctcgctgccaaaaaaaaagaaagaaggaaagaagattcccagctgattttcgccgtccccgcggcggatgtgtgtggtgaggctgacaacagcgcttgcttttcttgttgtttcgatttcttccag

Basic information

species Zea mays
transcript GRMZM5G856436_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g49150.2 (Oryza sativa), 5'ss of exon 1
GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctc---gacccttccgcgtctcctcgctgccaaaaaaaaagaaagaaggaaagaagattcccagctgattttcgccgtccccgcggcggatgtgtgtggtgaggctgacaacagcgcttgcttttcttgttgtttcgatttcttccag
||||||||||||||||||| ||||||||||||| || || || ||||||||||||||||||   || || |||||| |  ||  ||||||||||||||||||||  |||     |||   |   ||| ||   |  |             |  |         ||    |||   |||    |   | |||        |   || |    ||  | |     || | |   |  |  |||| ||||||| |||
GGCGATGGGGCGGCTGTTCGTGATGCACCTGGAAGGGAAGGTGTACAGCTGCAAGCACTGCCACACGCACCTCGGCCTCTCCTCCGACATCATCTCCAAGgttcgcctcttcagccccctcctttcttcttcttctc-------------gttgttgttgttgttgttggctagctttgtttgattcggcga-------gcacggcggatgtgggagcgattgtttcatggttgctgctttccatttcttgcag
















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|211161884|gb|FL207305.1|FL207305
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCGTCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211163480|gb|FL207315.1|FL207315
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|26558493|gb|CA830728.1|CA830728
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161885|gb|FL207306.1|FL207306
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161887|gb|FL207308.1|FL207308
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|22472703|gb|BU037183.1|BU037183
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211160285|gb|FL207293.1|FL207293
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161891|gb|FL207312.1|FL207312
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161881|gb|FL207302.1|FL207302
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|16927653|gb|BM080722.1|BM080722
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGAAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211160284|gb|FL207292.1|FL207292
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211458337|gb|FL363659.1|FL363659
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161888|gb|FL207309.1|FL207309
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGN
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|14243210|gb|BG840951.2|BG840951
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211163479|gb|FL207314.1|FL207314
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|67017876|gb|CO446625.1|CO446625
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|16917041|gb|BM073101.1|BM073101
EST:     TTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: TTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|21389991|gb|BQ528040.1|BQ528040
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|60341900|gb|DN208873.1|DN208873
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|31352331|gb|CD436688.1|CD436688
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161892|gb|FL207313.1|FL207313
EST:     GCAA-CACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161889|gb|FL207310.1|FL207310
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211160286|gb|FL207294.1|FL207294
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|31352347|gb|CD436704.1|CD436704
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|16925094|gb|BM078162.1|BM078162
EST:     GCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161880|gb|FL207301.1|FL207301
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|31351127|gb|CD435484.1|CD435484
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161886|gb|FL207307.1|FL207307
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|14242748|gb|BG840532.2|BG840532
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
EST: gi|211161883|gb|FL207304.1|FL207304
EST:     GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAG                         GCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT
genomic: GCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT

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), 44 (downstream exon)
Score: 101

GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 64

GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 74

GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcg ... tttcttccagGCCTTCCACTGCAGGCACGGGAAGGCGTACCTCTTCCATAAGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGATGGGGCGGCTGTTCCTGATGCACCTGGACGGCAACGTCTACAGCTGCAAGCACTGCAGGACCCAGCTCGGCGTTGCCAGCGACATCATCTCCAAGgttcctctcgacccttccgcgtctcctcgctgccaaaaaaaaagaaagaaggaaagaagattcccagctgattttcgccgtccccgcggcggatgtgtgtggtgaggctgacaacagcgcttgcttttcttgttgtttcgatttcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC