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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtcttatgaagtgctgagcattttcttggttttgcggatgtatataactagtctttggagcttatttataggattgatgtatcatccttgcacccc...

Basic information

species Zea mays
transcript GRMZM2G034143_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034143_T03 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 14
GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtcttatgaagtgctgagcattttcttggttttgcggatgtatataactagtctttggagcttatttataggattgatgtatcatccttgcacccc--
|||||||||| ||||| || || ||||| || ||||||||||||||||| ||| |||| ||||| || || |||||||| |||||||||||  |||||||||  |  |||  || |||||| |  |  || ||   | | | |   | || ||  |    |  |  |   |  ||          
GAAATTCAGCTGTTCAAGCTATATCCCTACTCTTGAAGAAGGGTGTACAGGAAACAAACATTATCTTTCTGAATCTTATATCAgtaagtctactgaagtgctttg-gtttcatttgttttgagtcttaatttattca-tttgtatggattgttgcttttttgaagctcataatctgatgatttgg

upper sequence: GRMZM2G034143_T03 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 5'ss of exon 14
GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtcttatgaagtgctgagcattttcttggt-tttgcggatgtatataactagtctttggagcttatttataggattgatgt-atcatccttgcacccc
|||||||||| ||||| || || || || || ||||| ||||||||||| ||| |||||||||| || || |||||||| |||||||||||  |||||||||||   |    |   | |||    || |  ||   | |  | ||     |||| |      | || | ||  |  | | ||   
GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctactgaagtgctgactttggattcattatttatttatttgcatggattgcatatgtgctctattgaagctcataatctgattgttttggtaca--
















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|211032140|gb|FL160201.1|FL160201
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|211032141|gb|FL160202.1|FL160202
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|14311434|gb|BG901189.1|BG901189
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|148943393|gb|EC888452.2|EC888452
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|211032143|gb|FL160204.1|FL160204
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|37385350|gb|CF629812.1|CF629812
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|60340284|gb|DN207257.1|DN207257
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|110957674|gb|EE177726.1|EE177726
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|24766852|gb|CA401999.1|CA401999
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|67012645|gb|CO441394.1|CO441394
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|78113248|gb|DV531642.1|DV531642
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
EST: gi|211032142|gb|FL160203.1|FL160203
EST:     TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCA                         GCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC
genomic: TGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATC

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: 47 (upstream exon), 49 (downstream exon)
Score: 87

GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATCGTTACTTCGGAGATTGAGTTTGGTCTAAATGATGATTTCCGTGTTGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATCGTTACTTCGGAGATTGAGTTTGGTCTAAATGATGATTTCCGTGTTGTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 72

GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATCGTTACTTCGGAGATTGAGTTTGGTCTAAATGATGATTTCCGTGTTGTGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 109

GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtctta ... gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATCGTTACTTCGGAGATTGAGTTTGGTCTAAATGATGATTTCCGTGTTGTGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATTCAGCAGTTCAGGCCATCTCCCTTCTATTGAAGAAGGGTGTACAAGAAGCAAATATTATATTCCTTAATCTTATTTCAgtaagtcttatgaagtgctgagcattttcttggttttgcggatgtatataactagtctttggagcttatttataggattgatgtatcatccttgcacccc

- - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA