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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT

Basic information

species Zea mays
transcript GRMZM2G102858_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcataca--ttacatcagctaagaagaaactgttttgactctttaac-tcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
  |    |||  | || |   | ||  | |||  |  | ||   |  ||  |  | ||   || || |   |   |  ||   |  || |  ||||    |||| |||||||| || ||  | ||||||||||| || ||||||||||||||||| |||||||| || |||||||||| ||||||||| || |||||||||||
-ggagcaaatagtgcatgat-tgagccagttgggac-atttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 3
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaact-cagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
 ||||    |||||    |  | | ||   ||   ||  |     |         | | | |||    |||      | | ||||  |  | |   | |||| |||||||| || || ||| | || |||||||||||||| ||||| ||||| |||||||| || |||||||| |  ||||||||||| || || || ||
atgttcatttgttaagtagtgttattttactgtgttttttaagttgatctgctgga-agtgcatacattaactgatgatttttttatccttgttcttgcagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGGAAATTGTTGGAACCTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 3
--------------ttgtttgaatgttacaaggcatc---agttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaac-----tcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
               | | | | | || |  |   ||      | |     || | ||||     ||||  | | | | |  |       || |     ||| ||| ||||||     ||||| ||||| || ||  || | ||||| || |||||||||||||||||||||||  || ||||||| ||||||||     ||||||| || ||         
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCG--------

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 3
--------------ttgtttgaatgttacaaggcatc---agttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaac-----tcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
               | | | | | || |  |   ||      | |     || | ||||     ||||  | | | | |  |       || |     ||| ||| ||||||     ||||| ||||| || ||  || | ||||| || |||||||||||||||||||||||  || ||||||| ||||||||     ||||||| || || ||||||||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
----------------------------------------------ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtca---aatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
                                              |  ||||  |||||||     | |  | | |||   |  |  | ||||     |   ||| |||| ||   ||| | | || |||    | ||||  |  |||| |||||||| ||  || | ||||| || ||||| |||||||||||||| ||| |||||||||| ||||||||||  |||||||| ||||| ||||||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatat--ttacatgtgtgattgtgttgtagagtctcctgaatgtactttac-tcctttaatatgcaattgt----aatcttggaa-cagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 2
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcat--acattacatcagctaagaagaaactgttttgactctttaact-cagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
 ||||    ||||     |  | | ||   ||   ||  || | |||  |  |      | | |||    |||        | ||||  |  | |  ||  ||| |||||||| || || ||| | || |||||||||||||| ||||| || || |||||||| || ||||||||||  ||||||||||| || || || ||
atgttcatttgttgagtagtgttattttactgtgttt--ttta-agttgatccgctggaagtgcatacattaactgatggtttttttatccttgttcctgtagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGAAAATTGTTGGAACCTCAAGATTGTGTGGCACATATTCTTCCTGTCATAGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
------------------------------------------------ttgtttgaatgttacaag---gcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
                                                 | ||||  | || ||      |||  ||| | |||   |  |  | | ||   | | |  |    ||  ||   || |   ||| |||     ||    |||| |||||||| ||  || | ||||| || ||||| |||||||||||||| ||| |||||||||| ||||||||||  |||||||| ||||| ||||||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctga-atgtactttcctcttttaata---tgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------------------------ttgtttgaatgttacaaggcatcagttatttgaaa-ttagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
                                                                                                |   | || | |    |     |  |||| || | |||  ||      ||    |   |||  |  ||| | |          || |  ||| |  |||||||||||||| ||| |||||||||| ||||| || ||||| |||||||| ||||||||||| || || |||||||  ||||  ||| | || ||||||||
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
                  | ||     | |     ||  || ||    | | |||| ||   ||  |   |     | || |      | || |  ||||| |||||||| ||  || ||||||| |||||||||||||||||||||||||| ||||||||||| || |||||||    ||| ||||| || || |||||
------------------gtattgaacactgagcgtttatttact-ctacagcatatat---atttgtcgaatttcatct-tacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaaga----agaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
    |  | |    ||      | ||| | |  |  |      ||||    |  || |||| |  |    |||    |   |   | |||||  || |  ||||| |||||||| ||  || ||||||| |||||||||||||||||||||||||| |||||||||||||| || ||||  ||||| ||||| || || |||||
---ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgaca-ttgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT

upper sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 4
ttgtttgaatgttacaaggcatcagttatt--tgaaattagttcacagtcaaatcatac--attacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
   |   || |||      | |  ||| ||   |  |||  || | | |  ||  ||       |  |  | |   |    ||  |||    | || |  ||||| |||||||| ||  |  ||||||| |||||||||||||| ||||| || ||| ||||||| || |||||||||| |||||||||||| || || |||||
-aatgacaaagttgtttttctttcgtttttgccggtatttttttatattggaagtatgatagccatttgggttgttagcttacaattt---attttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAAAGCTGTTGGAACCTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGT

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|18383985|gb|BM417185.1|BM417185
EST:     TCATTTGAAGNCAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATG                         NCCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGA
genomic: TCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGA
EST: gi|32866258|gb|CF005940.1|CF005940
EST:     TCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATG                         ACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGA
genomic: TCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGA
EST: gi|148969766|gb|EE020648.2|EE020648
EST:     TCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATG                         ACCAAGATTCAGTGCGACTATTGGCAGTTGA
genomic: TCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGA

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: 237

AGAGCTGCTGCATCCAATCTTGGGAAGTTCGCTGCAACAGTGGAACAAAGTCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 181

AGAGCTGCTGCATCCAATCTTGGGAAGTTCGCTGCAACAGTGGAACAAAGTCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 132

AGAGCTGCTGCATCCAATCTTGGGAAGTTCGCTGCAACAGTGGAACAAAGTCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 138

AGAGCTGCTGCATCCAATCTTGGGAAGTTCGCTGCAACAGTGGAACAAAGTCATTTGAAGACAGAAATCATGTCAATGTTTGATGATCTAACTCAAGATGgtacatgcta ... tttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
                                            ctttaac  putative branch site (score: 138)
                                          ctcttt  CT-rich tract
        atacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - ttgaatg
- - - - - - - - - gcatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaaa