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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT

Basic information

species Zea mays
transcript GRMZM2G147446_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 3'ss of exon 4
------actatttaagtgccactt---tttcatttggacttcggccctgtcatgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
      | |  ||||||   |      |  ||  |  | |||    |  | |  ||  |   |||      |||||||  ||||  || |||||      | | |||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||| |||||||||||||| || || || ||||||||||| || |
tttgtcatttcttaagttatagccaaatagcaccttaatttcttttcc-ttacctggacg-catagacaatacaattttaactc--ttctatttt-----cctttgcagTATGTTCATTTTCTCCAACGAAAGTACTCTCTGAACTCATTCAACCTCCTGGGTCACACTGCTCCAGCCCAAGCAGGATCCCTTCTGCTAGTGGGGCCCT

upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaat---ataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
  |   ||| || ||||   | | |      |  |   |||||  |    |||   | |      ||   ||||  ||  ||   |||||  |     |||||||||| |||||||||||| | |||||||| ||||||||||||||||||||||||||||| |||||||||||||| || || || |||||||| || || |
--tgaataattggcactccctaaatcatttgtttgtt-tgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT

upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
actatttaagtgccactttttcatttggacttcggccctgtca-tgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
      ||||||     |  || |  ||| |        ||   | ||   || |||||    | |  || |  |   |||||        | |  |||||||||| ||||  || || ||||||||||| || ||||||||||||||  |||| || || |||||||||||||| |   || | ||| |||| || || |
-----gtaagtgttctgtgctcttacggagtaacatatcgtttctttgtttaagataatactaata--ttggtgtggttttta--------catgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT

upper sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
actatttaagtgccactttttcatttggacttcggccctgtca--tgtgcccaatataatgggcacaatttagactcacttttatttctgctccttc--tgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
                               |  |  || | |  |  |    | | || |   |  ||| ||| | ||    | ||   ||| ||   |||||||||| |||| ||| || || |||||||| || | |||||||||||| ||||| || || |||||||| || ||||   |  |  || |||| || ||||
------------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT

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|149110810|gb|EE190620.2|EE190620
EST:     GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATAC                         TATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAAACTCCTG
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
EST: gi|78076134|gb|DV504568.1|DV504568
EST:     GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATAC                         TATGTCCATTTTCTCCCACGCAAGTACTCCCTGAACTCATTTCA-CCTCCT
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATT-CAACCTCCT
EST: gi|148986808|gb|EE030604.2|EE030604
EST:     GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCACCAATAC                         TATGTCCATTT
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTT
EST: gi|93282197|gb|EB674461.1|EB674461
EST:     GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATAC                         TATGTCCATTTTCTGGAACGCAAGTACTCACTGAACTCATTCAACCTCCT
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCT
EST: gi|78076922|gb|DV505356.1|DV505356
EST:     GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATAC                         TATGTCCATTTTCTCCCACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
EST: gi|149000630|gb|EE037833.2|EE037833
EST:     GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATAC                         TATGTCCATTTTCTCCCACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTG
EST: gi|148947730|gb|EC893211.2|EC893211
EST:     GTCTAATTGCTGCTGTTATAGCTGGTTGGAGCACAGCTTTGCAACAATAC                         TATGTCCATTTTCTCCAACGCAA
genomic: GTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAA

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: 48 (upstream exon), 46 (downstream exon)
Score: 70

TATAGGAGTTGCAGTCTGCACGGTTACTGATGTCAGTGTGAATGCAAGAGGTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

TATAGGAGTTGCAGTCTGCACGGTTACTGATGTCAGTGTGAATGCAAGAGGTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

TATAGGAGTTGCAGTCTGCACGGTTACTGATGTCAGTGTGAATGCAAGAGGTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 167

TATAGGAGTTGCAGTCTGCACGGTTACTGATGTCAGTGTGAATGCAAGAGGTCTAATTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTGCAACAATACgtgagtttta ... ccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
                         gactcac  putative branch site (score: 167)
                           ctcacttttatttctg  CT-rich tract
                              acttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT