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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgactgtaattcatgtgttataataattggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT

Basic information

species Zea mays
transcript GRMZM2G045330_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 6
acttgactgtaattcatgtgttataataattggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
  | || | ||| |  ||   | |  |   | |     ||| || |  |   |     ||| |   | |  || || |  ||||| | ||  |    ||| |||||||||||||||||||||| ||||| |||||||| || |||||||| |||||||||||||||||||| || |||||||||| |||||| |||||||
cttggattataactgttggcctctcttccctagttctgttatttcttcattttgctattttaacaaatagattgatgatctccttgtactattccaccagGTTCCTGGTGAACCGAACATATCATACATTTGCTCTCGCTATTATCGTGCTCCTGAGCTCATATTTGGTGCAACCGAGTATACAACTTCAATTGACATAT

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 6
acttgactgtaattcatgtgttataataattggactctt-tacttgtatacc-gtaaatctttgatccacatgttaatcagttccttatgctgctt--tgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
       | ||    |   || ||  |  ||||  ||   | ||  | | |   ||  | |||| ||   |     || | ||   ||   |  ||  |||||| |    |||||| | ||||| || |||||||| || || |||||||||||||| ||||| |||||||||||| | || || |||| |||  | || || |
--caatatatagaagaaaggtcat--tggttggggtcacatgctaatttgcttatagttatttgctcataaaaggtatgattttaataatttatttcatgtcagGTGGAGGGTGAATCAAACATTTCATACATATGTTCACGGTACTATCGTGCCCCAGAGCTAATATTTGGTGCGGCAGAATACACAACTTCTGTTGATATTT

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
-acttgactgtaattcatgtgttataataa--ttggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
 |  | ||  ||    ||   ||    | |  |||  | | |  ||  | | | | | |    || | |   |  |||  |  | |  ||  ||  |  |||| |    |||||| | || ||||| |||||||| || || | ||||||||| || || || ||||||||||| || ||||||||||||||||| || || |
catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcaga---atgtttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 5
--acttgactgtaattcatgtgttataataattggactct--ttacttg-tataccg-taaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
  |   | |  |  ||   ||   ||  ||||| |  |    ||| ||| ||| |   |||| | |        || ||||| | ||  ||         |||||| |    |||||| | ||||| || ||||||||||| || |||||||||||||| || || ||||||||||| || || || |||| |||  | || || |
agaaaggtcattggttggggttacatgctaatttgcttacggttatttgctatgctaataaaacatatggtatgattttaatgatttattttca------tgtcagGTGGAGGGTGAATCAAACATTTCATACATATGCTCACGGTACTATCGTGCCCCAGAACTAATATTTGGTGCAACAGAATACACAACTTCTGTTGATATTT

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 6
----acttgactgtaattcatgtgtta-taataattggactct-ttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
       |   |  || | |||| ||| | | | |  ||  ||  |||   | |  |  | |||   ||||      || |  |       ||  ||  |  |||| |    |||||| | || ||||| |||||||| || || | |||||| || || || ||||||||||| || || ||||||||||||||||| || || |
ttctgtattctttcaacttatgttttagtgagagtgtgagactactacccatcttaca-atatccaggatc-----atttactaaccttcaattttgtctcatcagGTCAAAGGTGAAGCTAATATATCATACATATGTTCACGGTTCTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTT

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 5
acttgactgtaattcatgtg---ttataataattggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
    |||| |    ||| |    | ||   | ||| |    ||  |||| | | || |   | | ||  || |||| |  | || ||| ||||      |||| ||   |||||| | ||||| |||||||| ||||| || | ||| ||||| || ||||||||||||||||| || ||||| |||| ||| || || || |
gtaagactttgtgacatataaactcattcgacttgtagcggttg-ttgttttctgtgatcttgtcatttac-tgttgaa-atttacttttgct------tcagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCT

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 6
-acttgactgtaattcatgtgttataataattggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgcttt--gtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
   || |  ||| |   |      ||  ||    | ||||| ||||| |    |   ||| ||||     |  |  |     | | |  |   |||   |||| ||   |||||| | |||||||| |||||||| ||||||| ||| || || ||||| ||||||||||| || || ||||||||||  ||||| || ||||
tctttcatggtagtcagtactcagtaggaag-aaagtctttgcttgttttttctt--tctatgatatctttcatgttttcaccatgaatccaattttcatcagGTTAAAGGTGAAGCAAACATATCATACATATGTTCTCGTTTCTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATAT

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|20508268|gb|BQ279947.1|BQ279947
EST:     GACTTTGGTAGTGCAAAAGTTCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCC
genomic: GACTTTGGTAGTGCAAAAGTTCTGgtatgttgtt ... gctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCC
EST: gi|67028577|gb|CO457326.1|CO457326
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCC
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtt ... gctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCC

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: 223

AATTAGTTCTGAATTGGTCTCGTCGTCTCTCTTTGATGTACAGGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtt ... gctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

AATTAGTTCTGAATTGGTCTCGTCGTCTCTCTTTGATGTACAGGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtt ... gctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

AATTAGTTCTGAATTGGTCTCGTCGTCTCTCTTTGATGTACAGGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtt ... gctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 122

AATTAGTTCTGAATTGGTCTCGTCGTCTCTCTTTGATGTACAGGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgtatgttgtt ... gctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT
                        tgttaat  putative branch site (score: 122)
                                           ctgcttt  putative PPT
       taaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgactgtaattcatgtgttataataattggactctttacttgtataccgtaaatctttgatccacatgttaatcagttccttatgctgctttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTACTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - -attcatg
- - - - - - - - - - - - - - - - - - - ttacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtta