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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcccactgtcctttgcctatttttctggtttatgaattagttgcacttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG

Basic information

species Zea mays
transcript GRMZM5G846811_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 1
------ctcccactgtcctttgcctatttttctggtttatgaattagttgcacttttag-tgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG
       |  || |    ||  |||  |||| |   ||||||||  ||||  | || ||  ||||  ||||     || | ||||  || |||||||  |||| ||||| ||||||||||| |||||||| ||||||||||||||||| |||||||||||||| || ||||||||||| || |||||||||||||
agttctgtaacagtaggattcacctcattttgtatcttatgaatcggttgtgccttgagacgatatgtgca-----ctcattgttcgcgtcattgct--tttgacagGATTATGTTCCGACGGTGTTTGACAACTTCAGTGCCAACGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 3'ss of exon 1
----ctcccactgtcctttgcctatttttctggtttatgaattagtt-gcacttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG
     |  | |           || ||| |       |   ||||   || ||| | || |  | | |  |   || |       |      | || |||  ||||| || ||||| || |||||||| |||||||| || || || ||||| ||||| ||||| |||||||||||  | ||||| || ||||
agggatggcgcgcaaggagatgtactttaccacagcgtctgttagacagcgcttcttgt-actcttacgatgtcctaagca----catgcccgttcgtttcgcagGATTACGTTCCTACCGTGTTTGACAACTTCAGCGCAAATGTAGTGGTCGATGGAAATACCGTCAACCTCGGGTTATGGGATACAGCAG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ04304 (Selaginella moellendorffii), 3'ss of exon 1
ctcccactgtcctttgcctatttttctggtttatgaattagttgcacttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG
                                     | || |    | ||     || |||  | |  || || ||    |       |||  | ||||||||| || || ||||| ||||||||||| |||||||| ||||| || ||||| || ||||| ||  | || ||||||||||| || |
------------------------------------gtgagattttttcttctctttagatg-ggaattctaaccgtgaatg-------tctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG

upper sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
ctcccactgtcctttgcctatttttctggtttatgaattagttgcacttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG
                               |  || || |||    | ||     |   |  |    |||  ||   |  |  || | || |   | |||| || ||||| || || |||||||||||||| ||||| || || || ||||| || ||||||||||| || |||||||||||||| |
------------------------------gtgagatttcgttttgttctttcctttttctcta----actctcttgggctgggatcgttcatcaac-agGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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|22545282|gb|BU097655.1|BU097655
EST:     TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACC                         GACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGAT
genomic: TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGAT
EST: gi|211082353|gb|FK946329.1|FK946329
EST:     TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACC                         GACTATGTTCVGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGAT
genomic: TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGAT
EST: gi|211082358|gb|FK946334.1|FK946334
EST:     TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACC                         GACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTTGTGGTTGA
genomic: TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTT-GTGGTTGA
EST: gi|211082360|gb|FK946336.1|FK946336
EST:     TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACC                         GACTATGTTCCGACAGTTGTTTGHTAACTTCAGTGCCAACGTTGTGGTTGA
genomic: TCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGT-GTTTGATAACTTCAGTGCCAACGTTGTGGTTGA

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: 193

GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACGGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACGGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACGGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACGGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctcct ... cttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG
                      cacttac  putative branch site (score: 283)
                                        ttgctctttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcccactgtcctttgcctatttttctggtttatgaattagttgcacttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- -ccactgt
- - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattgc