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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaccttagaaagtaccttcttcataattttgttgctatgtatttatagtcattttaattttaacatggtagctattagttgtttattttttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA

Basic information

species Zea mays
transcript GRMZM5G892742_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g25210.1 (Oryza sativa), 3'ss of exon 4
tgcaccttagaaagtaccttcttcataat-tttgttgctatgtatttatagtcatttt----aattttaacatggtagctattagttgtttattttttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA
   |   | | |  ||  || | ||       | |    || |||| ||  |  ||||    | ||| || ||  ||| |  |  |    ||  |||| |   |||||| ||| |||||||||||| |||||| ||||  ||||||||||||||||  ||||| ||||| || ||||||||||||||||  ||  ||||||||||
--tatgatggtatatatgttttgcacggcacatatcataatttattcatcattgttttttctattttgaatattctagtttctgatc---taaattttctcctagATTGCGAGAGTCGTGGAGAGATACCATGTCCTATTTGCAATGCTGGTCAGGAGCACGGATTTTACAAGGCAAATCAGATGACCCGTTGCAGTGCATGTCA
















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|22472922|gb|BU037402.1|BU037402
EST:     AGAAGTGACCGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
EST: gi|71439824|gb|DR820874.1|DR820874
EST:     AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
EST: gi|71438689|gb|DR819739.1|DR819739
EST:     AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGC
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGC
EST: gi|87155688|gb|DY400477.1|DY400477
EST:     AGAAGTGACCGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
EST: gi|148999746|gb|EE036749.2|EE036749
EST:     AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGAAGAGAAACCATGCCCTACATGCAATGCTTGGTCAG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCT-GGTCAG
EST: gi|71422780|gb|DR805839.1|DR805839
EST:     AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAAC-ATGCCCTACA
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACA
EST: gi|26558823|gb|CA831058.1|CA831058
EST:     AGAAGTGACCGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
EST: gi|166625660|gb|EG093344.1|EG093344
EST:     AGAAGTGACCGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCG
EST: gi|5847487|gb|AW000566.1|AW000566
EST:     AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG
EST: gi|71446190|gb|DR827240.1|DR827240
EST:     AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAG                         ATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGGCAAG
genomic: AGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGG

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: 61

TGGGAACTTGATTTGAGGTCTAAGTTTCCTGTACTTTTTGTACCAGAGAAAGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 140

TGGGAACTTGATTTGAGGTCTAAGTTTCCTGTACTTTTTGTACCAGAGAAAGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 84

TGGGAACTTGATTTGAGGTCTAAGTTTCCTGTACTTTTTGTACCAGAGAAAGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

TGGGAACTTGATTTGAGGTCTAAGTTTCCTGTACTTTTTGTACCAGAGAAAGAAGTGACTGTCAAGATTCCACATTCAGATATTATTGAAAAGTGCTCAGgtactgtgta ... tttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtcattttaattttaacatggtagctattagttgtttattttttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA
              ttttaac  putative branch site (score: 94)
                                   ttgtttatttttttt  putative PPT
                             tattagttgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaccttagaaagtaccttcttcataattttgttgctatgtatttatagtcattttaattttaacatggtagctattagttgtttattttttttgacagATTGTGAGGGTCGTGGAGAGAAACCATGCCCTACATGCAATGCTGGTCAGGCTCACGGGTTTTATAAAGCAAATCAGATGACCCAGTGTGGTGCATGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG