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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT

Basic information

species Zea mays
transcript GRMZM2G013079_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
       |||| |||   | |   |   | |  ||  | | ||       ||| ||||||||       | | ||||||||||   |||  |||||| |||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| || ||||||||||| || ||||| ||||| 
-------gtaacgttaactcccctatcttga--aatttaaatttgacttgtagcttgaagta------aatgtctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G43340.2 (Glycine max), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
     ||||    |    |||||      | || | |  |  | ||  |  ||          |  |     |||  |||   ||| | ||||    |||| |||| || ||||||||||||||||  ||||| ||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || |||
---gtaagtccactagacttctatgtgtgtgcataaaata--ttagtaaagaggccactcctcttctatgctcctcattgtgactt-tgtattt---tagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
     || |         || ||   |   |  |         |   || |    |  | | | | ||      |   |||  ||| | | ||  | |||| |||| ||||| |||||||||||||  ||||||||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || |||
---gtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctga-tcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G11330.1 (Glycine max), 3'ss of exon 8
--atgacaagta-------atgtttgtttctacactgtta-caaacatga-gttcagacactagattga--agtattaattgaggcctgc-ttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
  | | ||| ||       |||| ||    || | | ||| |||| | |    ||     |||   |    | | |   ||      |   ||  || || | |  |  | |||| |||| || ||||||||||||||||  ||||| ||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || |||
gtaagtcaactagacttctatgtgtgcgcataaaatattagcaaagaggctactcctcttctatgcttcccattgtggctttgtatttatgtttgactttgttttgtattttagGGATGTCAAATACCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G33700.1 (Glycine max), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
     || |    |    || ||   |   |  | |   |   |   || |    |    | |   ||      |   |||   || | | ||  | |||| ||||||| || |||||||||||||  ||||| ||||| || || || || ||||| ||||| ||||| || |||||||||||||| || || || |||
---gtaattccactggacttgtatttttgaatgagcccaatccctttcaatgttcttcgttgtggctttgtagttatctga-ttttgtttcttattgtagGGATGTTAAATATCATGAACCTGAGTTTTGGAAGTTTGGAGAAGAGGGGAACAAATATTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G22015.1 (Arabidopsis thaliana), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcct---gcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
      | ||||  |  | | |    ||||| |  |||   ||   | | |  |||    |||| |||  ||  |    |  |    ||||| |    | |||||  |  ||||||| |||||| ||||  ||||||||||| || ||||| || ||||| ||||| ||||| ||||| ||||| |||||||| || || |||
----gtaataatcctaatgtgtgtgttgttatat-catttttttgaatattctatt---ctatttatttgggtttctaaccagttttttctcaaaatgtgtagGACGGCCAAGTACCGTGAACCCGAGTTTTGGAAATTTGGAGAAGAAGGTAACAAATATTTCCGACATGCTACGGGACAGATTTATGCCATATCAAAGGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G77810.1 (Arabidopsis thaliana), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
           |  ||   | | |  ||   ||| | | |  |    | || | || |    |||  | |    ||  | |   |  |  | |  |  ||||  || |||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || || |||||                   
----------gtaattccatttgc-ttgagtcaagcttaaagtt--tctctggttttactggttagattattgttgagttagTTTATTGAACTGTTTCAGGACAGTAAAGTACCATGAACCTGAGTATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATC------------------

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 8
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
           |  ||   | | |  ||   ||| | | |  |    | || | || |    |||  | |    ||  | |   |  |  | |  |  ||||  || |||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || || ||||| |||||||| || || |||
----------gtaattccatttgc-ttgagtcaagcttaaagtt--tctctggttttactggttagattattgttgagttagtttattgaactgtttcagGACAGTAAAGTACCATGAACCTGAGTATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATCTATGCCATCTCCAAGGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 8
-------------------atgacaagtaatgtttgt-ttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcct-gcttgaaccttctctattcatat---agGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
                   |     | ||   | | | ||| ||  | ||     | |   ||   |  ||   ||    |  |  ||    |||  |       ||  ||  || | |   |||||||| |||||||||||||| || |||||||| ||||| ||||| || || || || ||||| ||||| || |||||||| ||||| || || ||||||
gtaatcctctcaggcttgtagattgattagaatctctcttcaactttctttttgcctttctttgtcattctttctttctttcctttttttccccttacacatttttttcctgctcgtcttctagGAATGTAAAGTACCATGAACCAGAATACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGAT

upper sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0031g03090.t01 (Vitis vinifera), 3'ss of exon 8
--------------------atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
                    ||||  || |  |      |  |    ||| |     ||| |   |    |  ||   | | || | |    | |||||      | |||  || |  |||| ||| ||||| ||||||||||| |||||||||||||| ||||| || ||||| ||||| || ||||| || |||||||| |||||||| || || |||
gtaagtcctactagctcttaatgaagagaacagggatccttgatttggttcctgggttgactatgg----tgaatctcaattttcaattcttcttgctttctttctttcttgtc-tgcagGACTGTGAAGTATCATGAACCTGAATACTGGAAATTTGGAGAGGAGGGGAATAAGTACTTTCGGCATGCAACCGGGCAGATTTATGCCATCTCAAAGGAT

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|71306960|gb|DR789635.1|DR789635
EST:     CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
genomic: CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
EST: gi|60358502|gb|DN225475.1|DN225475
EST:     CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
genomic: CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
EST: gi|5847319|gb|AW000398.1|AW000398
EST:     CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACT
genomic: CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACT
EST: gi|5525601|gb|AI861494.1|AI861494
EST:     CTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
genomic: CTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
EST: gi|60396395|gb|DN229264.1|DN229264
EST:     CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
genomic: CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
EST: gi|60398152|gb|DN230968.1|DN230968
EST:     CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
genomic: CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
EST: gi|91869350|gb|EB400347.1|EB400347
EST:     CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAA                         GAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA
genomic: CCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAA

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: 139

GAATGCTTGCCACTACCCTTGCTCGGCATAAATTGAAACCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

GAATGCTTGCCACTACCCTTGCTCGGCATAAATTGAAACCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

GAATGCTTGCCACTACCCTTGCTCGGCATAAATTGAAACCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 103

GAATGCTTGCCACTACCCTTGCTCGGCATAAATTGAAACCAAGAACTTATATTGGCTGCATGAAGTCAGGCCCAGTTCTCGCTGACAAgtaatgtttg ... attcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
               tattaat  putative branch site (score: 103)
                                     ccttctctattcat  putative PPT
        attgaagtattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - -tgtttgt
- - - - - - - - - - - - -ctgttac
- - - - - - - - - - - - - - - - - - - - - -cagacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgctt