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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 6
gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
||||  ||| ||  ||| ||  | ||||      | |  ||   |  ||   ||  || |     | || ||  |||| || ||   |||||||| |||||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||| ||||| ||||| ||||| |
gtactttcttctt-tccagcacacttgagtttggattttct---tcatgctaatcgctaa-----gattgatgttgaattgtttgcacagGTGATCGACAAGTCCTTTGGTTTTGACACTGCGGTGGAGGAGGCTCAGAGGGCCATCAATGCTGCTCATGTTGAGGCTGAGAGTGCAGAGAATGGCATTG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 8
-----gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtc--cattcctgattg-tagcttcatcctg--aactgctt-atgc-----agGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
     ||   || | || || |   ||   |  |||   |  |  |||      |   |||   |||||| ||  ||  | |||    ||  || ||||     |||| ||||| ||||| ||||| |||||||||||||| |||||||| ||  | || || ||||| || ||||| || ||||||||||  || || ||||| |
gtaaggttttattttcttctacattgtggctttaaactcataatttaaaccccattagcatcattgattggtaaatttcttctgctgtctctttgatgcttaatagGTTATTGATAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTTGAAAATGGCATAG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 7
------------------------------------gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
                                     ||  | || ||  | |||   || | ||||  |  ||  |    | ||||    ||| |||       |||  || ||  || |  ||||| ||||| ||||| ||||| |||||||||||||| || ||||| ||  | ||||| |||||||||||||| || || |||||  | ||||| || || |
gtgagcatgcttgaattggacatctgaagccttacaatagaagctactt-tgctgaaaatataaaaaggatttacttttaaactgtca---cctaattaa----ccatgttgtac--ctgaatcagGTTATTGATAAGTCATTTGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
gtacgatctgctcctcctgc------gtatttgaaaaaaaaatagctaattattgtc--cattcctgattg-tagcttcatcctgaa-----ctgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
||| | | |  |  |||| |      ||   |  |||   |  |  |||      |   |||   | |||| ||  ||  | |||        ||||||   |||| ||||| ||||| ||||| |||||||||||||| |||||||| ||  | || || ||||| || ||||| || ||||||||||  || || ||||| |
gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgctta-atagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
------------gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctga-------actgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
             ||  ||         ||||    |  |    ||  |       |||| |   |   |      |   |||   |||       |   || ||  |||| ||||||||||| ||||||||||| ||||| || |||||||| ||  | || || ||||| || ||||| || ||    |||| ||| |||||||| |
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 8
gtacg-atctgctcctcctgcgt-atttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
||| | ||||  | || |||| |  | |  | | || |    || || || |          |   | ||| |   |    |  || |||||||||| ||||| || ||||| |||||||||||||| || ||||| ||  | || || ||||| || ||||| || || || |||   ||||| || ||||
gtatgtatctctttctactgctttgtctctatagaagagctgtatttcttatgtggagaaattgagaacttgacttttg--tatttgtgcagGTGATAGACAAATCTTTTGGGTTTGACACTGCTGTAGAAGAGGCTCAACGAGCTATTAATGCAGCACATGTGGAAGCCGAGAGTATAGAGAATGGTATCG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------------gtacgatctgctcctcctgcgtatttgaaaaaaaaata--------gctaattattgtccattcctgattgtagct-----tcatcctgaact---gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
                                                        ||| |  | |       ||  |  ||||| |||           |  |||||| ||| | ||  || ||| |     | | |    |||   |||  | ||||| ||||||||||| ||||| |||||||||||||| |||||||||||  | || || ||||| || ||||| ||  ||||||||   |||||  | || |
gtacatctctttgtttccttaattgctgattataggaccggttggatattacacctgatttattgcatagatataaattcaaaaacaatttttttcctattttttattgaccaattctctttttagttgatttttacctccgactattgctggtacagGTTATTGACAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCCCAACGTGCTATTAATGCAGCACATGTTGAATCTGAAAGTATCGAGAATTGTATTG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------gtacgatctgctcctcctgcgtatttgaaaaaaaaat---agctaattattgtccattcctgattgtagcttcatcctgaactgctt--atg--cagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
                               |  |  | |        ||| |||||  | |         |  | |||  ||| | |||    ||||  ||   |   ||  || ||  |||  ||| | ||||| ||||| ||||||||||||||||||||||| || || ||  | || |||||||| |||||||| || || |||||| |  | || ||  | |
gtactatacatcatccctactacacagtgacgcgctttttcacatgtgtgcttatttccacatgttgcctgaattcattcgtgtgcgttctgacttgtt-ctcttttgggatttgtttcaatgaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG

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|116813643|gb|EC856113.1|EC856113
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|33099629|gb|CF059589.1|CF059589
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     TCAAGTGCTCTGGTGTCCGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCCTTTGGATTTGACACT
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACT
EST: gi|87153260|gb|DY398049.1|DY398049
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|211450005|gb|FL281917.1|FL281917
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG
EST: gi|211450006|gb|FL281918.1|FL281918
EST:     TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCG                         GTGATTGACAAGTCGTTTGGATTCGACACTGCTGTGGAGGAGGCCCAGAGG
genomic: TCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGG

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: 38 (upstream exon), 47 (downstream exon)
Score: 27

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 226

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 53

GAAGTCCGGAGACGGGGTCTCAAGTGCTCTGTTGTCGGTGTCCCAAAGACTATTGATAACGACATCGCGgtacgatctg ... gcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG
                   tcctgat  putative branch site (score: 53)
     taattattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctgaactgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA