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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG

Basic information

species Zea mays
transcript GRMZM2G044819_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 5
gtagaggtaacacatttcgtcaaagtttctgggcttcattgatgag----------aactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
|||  | ||| |||||| ||||   || ||| | | |   | ||||          || ||| ||||||||   |||| ||||||||||||||||||||||||||||| || |||||||||| | ||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||
gtattgttaagacattttgtcagctttactgtggtcctgagctgagagaagataataaatcttattcatgtccatgaacagTGAAATATATGGAAGAGAATTGGTGGATCTACGGAAAGAAAGTAGATGGGAGTTCCTTAATACCCTTTTCTCTGTGTCAGAAGCTGTTATGTTCATGCAG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 5
------------------------------gtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
                              ||||| || |   ||         |  |      |||  |  ||  | ||  | || || |        ||||| || ||||| |||||| ||||||||||||| || || | |||||||||||| || ||||| || || ||||| || ||||||||    | |||||||
gtgtgcatgttcacacacattattagcttagtagatgtcatttatcgaaaaccggagtaataatttctgtagtgcta-cttaattttatatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 4
-------------------------gtagaggtaacacatttcgtcaaagtt---tctgggcttcatt--gatgagaactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
                         |||     ||  || ||    ||  ||   | ||  ||| |||   |     ||   | || ||||   || | ||||| || ||||| |||||| |||||||||||||| || | | |||||||||||| || || ||  | |||||||| || ||||||||    | |||||||
agactatataagctgattagtgcttgtattttgaaatcaattaaataatattcagtttgccctttatttcaagtgttacctaattttatgtgcatgga-agTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 5
-------------------------gtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaa--ctctaattcatgtttttga--atagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
                         |   ||   |     || ||||||   |   |   |  ||  ||      || | | |  ||| |   |    ||||| || ||||| |||||| ||||||||||||| || || | |||||||||||| || ||||| || || ||||| || ||||||||    | |||||||
gcatgcatgctcacacacattaatagcttagtagatgtcatttgtcaaaaactggagtaatagtttctgtagtgccttttaattttgtatgcaatggaagTGAGATGTATGGGAGAGAACTGGTGGACCTGCGAAAGGAGAGTCGATGGGAGTTTCTCAATACACTGTTTTCTGTGTCTGAAGCTGTGGCCTACATGCAG

upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtagaggtaacacatttcgtcaa-------agtttctgggcttcattgatgagaactctaattcatgtttt-tgaat---agTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
                   |    ||||     || |  ||       |      |||    |||    |||   |   || |  || | || ||   ||||| || ||||| || ||| ||||||| ||||| || |||| ||||||||  ||||| ||||| || ||||||||||||||||| ||    || ||||||
gtaccctagattttcccgatgtttgtaatttgatttgctaattgtagcaagactagggtaatattttctagagtgcctgttaactttctatgcatggcagTGAGATGTATGGGAGGGAACTGGTGGATCTGCGAAACGAAAGTCGATGGGTATTCCTCAATACACTATTCTCTGTTTCAGAAGCAGTGGCTTTTATGCAG

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|71442993|gb|DR824043.1|DR824043
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|32937883|gb|CF042702.1|CF042702
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|17970200|gb|BM276964.1|BM276964
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 105

TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 79

TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 115

TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcaaagtttctgggcttcattgatgagaactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
                                ctctaat  putative branch site (score: 115)
                                          tgttttt  putative PPT
                                   taattcatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG