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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttggtatgcag

Basic information

species Zea mays
transcript GRMZM2G083095_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 2
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattga-------aacgtgcagtctgatagcaggctc----tttgtgcttttgtctttggtatgcag--
||| ||||| |||||||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||||||| || ||||| || ||||| |||| ||| |    |   |||    | |||||||       ||| ||  | ||||| |||||||     ||  ||| ||||  | ||  ||||    
ATCTTTTGCTGGTGAACTGCTTGAGAAGGCCGAGGAGCTTATCAGGATGGGGTTGCATCCAAGTGAGATCATCATTGGCTACACCAAGGCCATTAATAAGgttacttaccctcccgattgagctggccttatattgattaaaaaaacctgttgcctgatggcaggctagttattcatgcatttgcatctgcaatgcgcag

upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 2
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgactt-gccccctgactctggcttttgtaatat----tgaaacgtgcagtctgatag-caggctctttgtgcttttgtctttggtatgcag
 || ||||| || || || ||  ||   || ||||| || ||||||||||| |||||||| || |||||||||| ||| ||||||||||| |||||||||||   ||       |||     || || || || |    | ||| || ||   || |   |   |||  | |  |||  | ||| || | |||
TTCATTTGCTGGGGAGCTCCTGCAGGGTGCCGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCAATCAACAAGgttttttcagtttttgatgaaagccttagtgatctgtctttaaatgt-catattgctgctctctctccctctaatttcttgttttgt-ttcag

upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 2
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatag-caggctctttgtgcttttgtctttggtatgcag
 || ||||| || ||||| ||  ||   |||||||| || ||||||||||| |||||||| || |||||||||| ||| ||||||||||| |||||||||||   |||      | ||  | | ||    || || ||| || ||   || |   |   ||  || |  | |  | ||| || | |||
TTCATTTGCTGGGGAACTCCTGCAGGGTGCTGAGGAACTTATCAGGATGGGTTTGCATCCGAGCGAGATCATCAGTGGATACACTAAAGCGATCAACAAGgt--tttgatgagagccttagtcattc---atttttaaatgt-catattgctgctctctcttcttctaatgtattgttttgtgt-cag

upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT3G03960.1 (Arabidopsis thaliana), 5'ss of exon 2
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttgg--tatgcag
 || ||||| |||||||| ||| | || ||||||||||| |||||||||||  | ||||| ||||||||||| | ||| || ||||||||  ||| ||||||   |     ||||| |     ||||||  | || ||       ||||   || |         |||| |||  ||| |  |||||||
CTCCTTTGCTGGTGAACTTCTTCAAAACGCTGAGGAGCTTATCAGGATGGGACTTCATCCGAGTGAGATCATTAGTGGATATACTAAAGCTGTCAGCAAGgttggtgaatacctgaattactgttttgtgcttttcaatttgtttgtcttg-agtatttgacgaatgctattggattttgattatgcag

upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 2
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgact---tgccccctgactctggcttttg-----taatattgaaacgtgca---gtctgatagcaggctcttt--gtgcttttgtctttggtatgcag
 || ||||| || || || ||  | || ||||||||||| |||||||||||  |||| || ||||||||||||| ||| ||| | |||||||| || |||||  ||   |||   || |  ||   ||||      || | ||    | || |    | |     || ||| ||      || |     |  || | |||
TTCTTTTGCTGGAGAGCTCCTCCAAAATGCTGAGGAGCTTATCAGGATGGGGCTGCACCCGAGTGAGATCATCAGTGGATACTCAAAAGCCATTAATAAGgtttctccatgcttgctaatgctttgttttaacaactagtcttctcccctggatgaatttctagacatgctattctgactctctctctctctgtcttcag

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|211339975|gb|FL217825.1|FL217825
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|148995430|gb|EE034628.2|EE034628
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|71431587|gb|DR812637.1|DR812637
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|211342365|gb|FL217838.1|FL217838
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTNGGAGGATCTTNGNTGAGAAAGGCTCAGAGAACATGG
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTT-GGAGGATCTT-GTTGAGAAAGGCTCAGAGAACATGG
EST: gi|211339980|gb|FL217830.1|FL217830
EST:     GCTTGCATCCCAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAAAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|148987524|gb|EE031386.2|EE031386
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|211339983|gb|FL217833.1|FL217833
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|22715295|gb|BU197687.1|BU197687
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|87157134|gb|DY401923.1|DY401923
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|211339979|gb|FL217829.1|FL217829
EST:     GCTTGCATCCCAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGGTTGAGAAAGGCTCCGAGAACA
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTG-TTGAGAAAGGCTCAGAGAACA
EST: gi|148932523|gb|EC876316.2|EC876316
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|211342367|gb|FL217840.1|FL217840
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGANGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGA
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGA-GATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGA
EST: gi|211342369|gb|FL217842.1|FL217842
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: -CTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|149105115|gb|EE290598.2|EE290598
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|21760124|gb|BQ635665.1|BQ635665
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|211339978|gb|FL217828.1|FL217828
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTNGT-GAGAAAGGCTCAGAGAACATGGA
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTT-GTTGAGAAAGGCTCAGAGAACATGGA
EST: gi|26559613|gb|CA831848.1|CA831848
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|211342363|gb|FL217836.1|FL217836
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|22935567|gb|BU571842.1|BU571842
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
EST: gi|149015148|gb|EE044917.2|EE044917
EST:     GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAG                         ACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT
genomic: GCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGAT

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: 142

ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGA


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

ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgcc ... tggtatgcagACAATTGAGATCTTGGAGGATCTTGTTGAGAAAGGCTCAGAGAACATGGATGTGAGAAACAAGGAGGACGTTGTGTTGAGGATGAGATCCGCTGTCGCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGTTTGCCGGTGAACTGCTTGAGAAGGCTGAGGAGCTCATCAGGATGGGCTTGCATCCAAGTGAGATCATCATTGGCTACACTAAAGCCATCAACAAGgtgacttgccccctgactctggcttttgtaatattgaaacgtgcagtctgatagcaggctctttgtgcttttgtctttggtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA