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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG

Basic information

species Zea mays
transcript GRMZM2G164352_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcag-ttaagtgcatcaccactaacaaat-gctacttgcttgtact--cttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
    || | |         ||||||  ||  ||||||    |  |   | ||      || |      |||  | |  || |  | | | |   | || |  ||||||| ||||||||||||||||| |||||||| |||||| |||||||||| ||||| |||||||| ||||| || || ||
--aaagatacatagaaaaaataatt--ttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 3
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaat-gctacttgcttgtact--cttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
    |||| | | ||    || | || |   |||  |  |||||     ||      || |      |||  | |  || |  ||| | |   | || |  ||||||| ||||||||||||||||| |||||||| |||||| |||||||||| ||||| |||||||| ||||| || || ||
--aaagttac-atagaaaaattaattttgcttttgccgtcttgtattgcttcgaaaaatgaatttctacatcttgtcacatagttgaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 3
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtt---tagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
                        |  |||  | || |   | ||    | | |  |  ||     || |||||||   |  ||||||| |||   |    ||||||| || |||||||| || ||||||||||| |||||| | || ||||| ||||| || || || ||||||||||| ||
-----------------------gtgattatgtctgtaggcttttatgctgatgatctacatttaaaagaaatgcttaatctttgtactttttcactgagcagGATAAGTCTTGGCGTGTGCGCTATATGGTTGCAAATCAACTCTACGAGCTTTGTGAAGCCGTGGGACCTGAGCCTACTAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
-ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
        | |||  |  | |||||| || |       |  | |  |      | |          | |  | ||    |      |  | |  ||   ||||||| || ||||||||||| ||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||
caaactcatactattgagtcataatt-ctcataaaaatagttagaagtgtcacaatatggtttatttgatcattgtgtatgagaaattttttcctgaacagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactct----tttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG--------------------
                                                                 || || ||  |  |  | |  | | |    ||   | ||||||| || ||||||||||| ||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||                    
----------------------------------------------------------------gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
-------------------ttgtagttgctagag------gttgataatttcttagttttgcaacttgttgc-----------agttaagtg--catcaccactaacaaatgctacttgcttgtactct----tttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
                    | |||| ||| |          | ||| | | | || | |  |  ||||||            || ||||    ||| |     | || ||  | ||  | |  | | |    ||   | ||||||| || ||||||||||| ||||||||||| ||||||||||||||||| ||||| |                      
cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 3
ttgtagttgctagaggttgataatttcttagttttgca--acttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
 |  |     |  |  | ||| || |    ||  | ||  || | || |   ||  |    |     |   | ||     ||  || || | | | |   |||| | ||| ||||||||||| || ||||||||  |||||||||||||||| ||| | ||||| || |||||  |||| ||
-ttaaacaaatcaatatcgatgatattcaggtcattcattacatcttccgtctactttttactttttttttatatatatttttattttattgtgt-gaacagGACAGATCTTGGCGTGTTCGCTACATGGTTGCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAAGCTACCAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 3
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
                                            |     | | |   | |    |  |   ||||  |     || |   ||| |  |||| || || ||||| || |||||||||||||| |||||| ||||||| ||||||||  ||||||| || ||   ||| ||
-------------------------------------------gtatgtctcattcttttattgttc-ctgttgctgat--gcggtgcgtgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ10709 (Selaginella moellendorffii), 3'ss of exon 3
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
                                         |||  || |    |      ||  |  |  ||||     |   ||  |  ||| |  |||| || || ||||| || |||||||||||||| |||||| ||||||| ||||||||  ||||||| || ||   ||| ||
--------------------------------------gtatgtctcattcttttattgttcctgttgctgatgcg----gtgcgtgtttgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG

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|33091965|gb|CF051959.1|CF051959
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32940030|gb|CF044849.1|CF044849
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32831601|gb|CD971279.1|CD971279
EST:     CACAAGATTGCGTA-CACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|211403483|gb|FL417168.1|FL417168
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32938569|gb|CF043388.1|CF043388
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|22935744|gb|BU572019.1|BU572019
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32830645|gb|CD970323.1|CD970323
EST:     CACAAGATTGCGTA-CNCACATTCTTCCAGTCATTGTCAATTTCTCC-AG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAANTCAAT-ATATGAGCT
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAA-TCAATTATATGAGCT
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|211356091|gb|FL413289.1|FL413289
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTA
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTA
EST: gi|32847343|gb|CD987024.1|CD987024
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|211150174|gb|FL390449.1|FL390449
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|31353403|gb|CD437760.1|CD437760
EST:     ACAAGATTGCGTAGCACACATTCTTCCAGTCATTTGTCA-TTTCTCCCAG                         GATAAATCATGGCGTGTT
genomic: ACAAGATTGCGTAGCACACATTCTTCCAGTCATT-GTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTT
EST: gi|32829962|gb|CD969640.1|CD969640
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|32851452|gb|CD991133.1|CD991133
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|21088918|gb|BQ401231.1|BQ401231
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATA
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATA
EST: gi|211520937|gb|FL382784.1|FL382784
EST:     CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: CACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     TTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATCGTGTGTTCGTTATATGGTCGCCAATCAATTATATGAGCTC
genomic: TTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTC

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: 364

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG
                 cactaac  putative branch site (score: 208)
                                          ctcttttgttt  putative PPT
                                             ttttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactcttttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT