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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaaccctagaccccatgtacttactctcttttgtggttgtaattggcctacctacctaattaagctgtcgagtcactttcagtaatt...

Basic information

species Zea mays
transcript GRMZM2G029566_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 5'ss of exon 5
GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaacc-ctagaccccatgtacttactctcttttgtggttgtaattggcctacctacctaat-taagctg---tcgagtcactttcagtaatt------------------------------------------------------------------------------------------------
 || ||||| |||||||||||| | ||    |||||||||||||| ||  |||||||||||||||| |||||||||||||| ||||||| |||| || ||| |   ||| ||  | |  ||      ||| |||| | |||||     || |  | |    | |||    |    || |||                                                                                                
AGGGCAAGGCCATCCAACAGGAGATTCTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttcttacaaacctcttgactcacagtatttggtattcttga--actgttattgacatacctgttgcatgtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcag

upper sequence: GRMZM2G029566_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT1G12050.1 (Arabidopsis thaliana), 5'ss of exon 6
GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaaccctagaccccatgtacttactctcttttgtggttgtaattggcctacctacctaattaagctgtcgagtcactttcagtaatt----------------------
 || || || ||||||  ||||||||| |  || |||||||| || ||| |||| ||||||||||||||||||||||| ||| ||| |     |||        || | ||  | |    ||     ||   ||   |      ||| |||||   |   | || |  ||    |                       
AGGTCAGGGCCATCCACAAGGAAACTCTGAACCATATTTTGGACCTTCGAAGAAACTTGATTTTGAGCTTGAGATGgtaagcatctgatg---cctcagttatgtggatttgttttacaatgattcggttgatgctttttggtgctagttaaga-ataacggcattgacaaacctctcttttatcacatgatattcag
















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|211126134|gb|FL125776.1|FL125776
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|71328229|gb|DR800748.1|DR800748
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|149044247|gb|EE047493.2|EE047493
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|149101399|gb|EE187518.2|EE187518
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAAT
EST: gi|148969714|gb|EE020586.2|EE020586
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|60348819|gb|DN215792.1|DN215792
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|148932701|gb|EC876670.2|EC876670
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGGTC-AGGGAATGAATTANGCAAACCTATTGATATTAA
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGG-TCCAGGGAATGAATTAGGCAAACCTATTGATATTAA
EST: gi|148940815|gb|EC885642.2|EC885642
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAAGCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|148964333|gb|EC905725.2|EC905725
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|78124353|gb|DV542737.1|DV542737
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTACGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|148956082|gb|EC901838.2|EC901838
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|148955041|gb|EC900548.2|EC900548
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGGCCCGGGAATGAATTAGGCAAA
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAA
EST: gi|148983240|gb|EE029206.2|EE029206
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAA
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAA
EST: gi|148949167|gb|EC894603.2|EC894603
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTG
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTG
EST: gi|71421618|gb|DR805518.1|DR805518
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATT
EST: gi|148941367|gb|EC886277.2|EC886277
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGGCCAGGGAATGAATTAGGCAAAGCTATTG
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTG
EST: gi|149009361|gb|EE041411.2|EE041411
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|148946154|gb|EC891448.2|EC891448
EST:     CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
genomic: CCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAAT
EST: gi|89764162|gb|DY691069.1|DY691069
EST:     CGCCTC-TTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAA
genomic: CGC-TCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAA

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), 48 (downstream exon)
Score: 347

GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 190

GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2179

GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgctttcagGCTGCCATTGTTGGTCCAGGGAATGAATTAGGCAAACCTATTGATATTAATGACGCCGAAGAACATATTTTTGGCCTAACTTTGATGAATGATTGGAGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaaccctagaccccatgtacttactctcttttgtggttgtaattggcctacctacctaattaagctgtcgagtcactttcagtaatt

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG