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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG

Basic information

species Zea mays
transcript GRMZM2G044348_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
---gtaattggggctagcccttgcattttgaga-gcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
     |||   |  |     |||  || | |   |  | | | | ||||| |  || || ||    ||    | | ||| | |||    | |    |||| |||| |||||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || || ||||| || |||||||||||||||
gctacaat-aagattcatatttgttttgtaatttgtttttcattcattttttcatc-ttcatggtctttgctt-tgaat-cttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
gtaattggggctagcccttgcattttgagagcatctgaattattttatg-ttcattaattacattcatatg----taaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
     |  | |      |   |  || ||   ||     | ||| |||   || ||  ||   |  |||||    |  |  |  ||    |  |   |||| |||| ||| || ||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| || |||||||||||||||
-----ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 7
--gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
    | ||      ||  |   ||| |      ||| || || ||| | | ||  ||  ||  ||       |  |  |  ||    |  |   |||| |||| ||| || ||||||||||||||||||||||| |||||||||||||| ||||| || || || ||||| || |||||||||||||||
agtcagttattaaaagatcaaacatatgcttttcat-tgtataattctctcttt-ttgtttcaatatggtctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatg-------cattt----ttccttttcctt--tttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
     || ||   ||      |||  ||   ||  |  ||  |    || |       ||  | |||| | || |||||       ||||     ||  || | |||   || ||||  ||||| ||| | ||||| || |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||| |||
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
gtaattggggctagcccttgcattttgagagcatctgaattattttatgttca--ttaattacattcatatgtaaatgc--atttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
    |||  || ||   ||   |          | ||  |  |  |   ||||  ||  ||  | |  || || | |    |  |      || |   || ||||  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || ||||||||||| || |||
----ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: PP1S47_5V6.2 (Physcomitrella patens), 3'ss of exon 7
-gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
 ||   || |   ||       | | |  |||  |  | ||| |    ||   |||||||         | | |     |  |             | ||||  ||||| ||  | || ||||| ||||||||||||||||| || || ||||| || ||||| || || ||||||||||| || |||
ggtttgtgtgaaaaggtgcaagagtgtt-gagttttgggattgtaaattggcaattaattggggaggagtttgagatgttggtggtcacgatggagtgcagGCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG

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|93015394|gb|EB640914.1|EB640914
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|149100817|gb|EE186911.2|EE186911
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATG
EST: gi|148943973|gb|EC889054.2|EC889054
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTTCTGG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTT-CTGG

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: 180

GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 258

GGGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
      cattaat  putative branch site (score: 258)
                             tgcatttttccttttc  putative PPT
       attaattacattcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG

- - -tggggct
- - - - - - - - -ttgcatt
- - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca