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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcagaattatctttccacactgttatcatgttgacattctttattccactgagtctaaatgtttctgtgttcatcattattatttctccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA

Basic information

species Zea mays
transcript GRMZM2G088088_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 7
-tttcagaattatctttccacactgttatcatgttgacattctttattccactgagtctaaatgtt-tctgtgttcatcattattatttc--tccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA
 | ||  ||||     |  ||   ||| ||| |     |||    ||   | |   | || ||||| |||| ||||||  ||  | | ||  |   | |||||||||||||| ||  ||||||| |||||||| || ||||| ||  |||| | ||| || |||||||||||||||||||||||||||||||| ||||||||||
ctctctcaattgctgcttgactacgttctcaagaaagaattgac-ataagatt---tttatatgttatctgggttcattgttcatctctcaattgctgctgcagTGTGTCATCGATCATCAAGCTCTTCCATGTCTCTTGAACCTCTTGACCAACAATCATAAGAAAAGCATCAAGAAAGAAGCATGCTGGACTATCTCAAACA

upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 7
tttcagaattatctttccacactgttatcatgttgacattctttat-tccactgagtc--taaatgtttctgtgttcatcattattatttctccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA
    |    ||| ||    ||||  |  ||   ||       || | |  |||  ||   |   |||  ||    || |  || |  | |   |||    ||||   ||||  | ||||| || ||||| || ||| |   ||||||||| | ||| ||||||||||| |||||||||||||| || ||||| || || || |
---gacttctattttataccactcgtcccagaatggttcaacttgtgttgactttgttcttgcttgtaactaacatccttcttgtattgttgtcttggatcagTTCATCATCAATAATCAGGCCCTTCCCTGTCTTCTTGCTCTTCTGACCAACAATCACAAGAAAAGTATCAAGAAAGAAGCCTGTTGGACTATTTCCAATA

upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S165_51V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------tttcagaattat--ctttccacactgttatcatg-ttgacattctttattccactgagtctaaatgtttctgtgttcatcattattatttctcct-tcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA
                                                |||| | || |    | | ||      | | | | | | ||  | ||||| ||||     |       || ||  |  | |      | | | || ||  |||||   |||| |||   || ||  | || |||||  |    ||  |||| | |||||||||||| ||||| |||||||||||||| ||||| ||||| ||||
gtatccatacaagatctgaaatcattgcttcgctgtttcttttcaacatttctgcatcaaagttgttcatgtgtatgttacggtcgtcacccattatttcactttccatcccgtcatcagtagtgtttacgtgcgtgtttactgtcgcgcagTTCATCATCGACTGCCAGGCCTTGCCCTGCCTGCTCGCACTATTGACCAACAACCACAAGAAGAGCATTAAGAAAGAAGCATGTTGGACTATCTCCAACA

upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S43_141V6.1 (Physcomitrella patens), 3'ss of exon 8
--tttcagaattatctttccacactgtt-atcatgttgacattctttattccactgagtctaaatgtttctgtgttcatcattattatttctccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA
  | |      || |  | |    | || |  ||   |  |     ||         | || ||  ||| |||  |   |  ||||  |  |  ||    ||||   ||||  ||||||| || || || || ||| |   |||||| || | |||||||||||||||||| || || ||||| |||||||| ||||| ||||
cctctttttggtagcaatacgtgttttttaaaattcagtaaggaaataagggggacggcctgaa-atttgtgtactttcctctattgctgtt--ttgtatcagTTCATCATCAACAATCAGGCCCTCCCGTGTCTTCTCGCTCTTCTCACCAACAACCACAAGAAAAGCATTAAAAAGGAAGCCTGCTGGACTATCTCCAACA

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|211452350|gb|FL292615.1|FL292615
EST:     CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
EST: gi|6564217|gb|AW231839.1|AW231839
EST:     CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
EST: gi|211452354|gb|FL292619.1|FL292619
EST:     TCTTCGCACGGTGGGTAACATTGTAAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATG
genomic: TCTTCGCACGGTGGGTAACATTGTAA-CTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATG
EST: gi|213179381|gb|FM182985.1|FM182985
EST:     CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
EST: gi|6587581|gb|AW244899.1|AW244899
EST:     CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
EST: gi|211452351|gb|FL292616.1|FL292616
EST:     CTCTTCGCACGGTGGGTAACATTGNAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATC
EST: gi|211452349|gb|FL292614.1|FL292614
EST:     CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
EST: gi|33097597|gb|CF057557.1|CF057557
EST:     CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG                         TGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC
genomic: CTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACC

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: 523

GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 630

GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 558

GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 485

GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAGgtaaactcaa ... cttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccactgagtctaaatgtttctgtgttcatcattattatttctccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA
         gtctaaa  putative branch site (score: 485)
                              tcattattatttctcc  putative PPT
                          ttcatcattattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcagaattatctttccacactgttatcatgttgacattctttattccactgagtctaaatgtttctgtgttcatcattattatttctccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAATCTTCTGACTACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACGATCTCAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - ccacact
- - - - - - - - - - - - - - -atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatc