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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcccgtccctctcatttcctcctccgcgttgtcattgtttcgtttctttaaagctccatataactagttttcgtgtattcgacctcgaaaatg...

Basic information

species Zea mays
transcript GRMZM2G085960_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085960_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 5'ss of exon 1
---GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcccgtccctctcatttcctcctccgcgttgtcattgt-ttcgtttctttaaagctccatataa---ctagttttcgtgtattcgacctcgaaaatg
   | | |      || |   |    ||  ||| | | ||||| |  | |||   |||||| || ||| ||||||||||||||||| ||||||||||||||||||  ||| |   |||   || | | |  |  | | |||   |  |  | |||||||      |  || | |   || || |      ||     |||  ||   
AGAGAGAGAGAGAGAGAGTTAGTTTTGGGTGGATTTGTGATGGGGTCGAACG---AGCAGATCCACCGGGACAAGCTCATCATCGACACGGATCCCGGCATCGgtgagtccct--tcctcttcctcttcctcatctcattgcgctcatactagtttcttcctgatttgatttcaattcttgtgtggaaacatctcctctcccaac--
















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|74241088|gb|DT649002.1|DT649002
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|32797780|gb|CD950016.1|CD950016
EST:     GATCCGGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: GATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|93013944|gb|EB639464.1|EB639464
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|211348352|gb|FL160894.1|FL160894
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|211348356|gb|FL160898.1|FL160898
EST:     CCAGCAGACCCGCCGCGAYAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|78105353|gb|DV523771.1|DV523771
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|78103961|gb|DV522379.1|DV522379
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|32797544|gb|CD949780.1|CD949780
EST:     GATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: GATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|32847882|gb|CD987563.1|CD987563
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|71448364|gb|DR829414.1|DR829414
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|91048127|gb|EB158545.1|EB158545
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|93017218|gb|EB642738.1|EB642738
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|74238611|gb|DT646525.1|DT646525
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|149058761|gb|EE156779.2|EE156779
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|16925487|gb|BM078555.1|BM078555
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCATAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|71432393|gb|DR813443.1|DR813443
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|211348354|gb|FL160896.1|FL160896
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|86474150|gb|DY240520.1|DY240520
EST:     CCAGCAAACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         AAGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|211348353|gb|FL160895.1|FL160895
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATKGCGTTCAGAGCACATACTCTGGGAAATC
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGG-AAATC
EST: gi|78104295|gb|DV522713.1|DV522713
EST:     CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: CCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|32789762|gb|CD941998.1|CD941998
EST:     GATCCCGGCATCG                         ATGATAGCATGGCCATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: GATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
EST: gi|32797907|gb|CD950143.1|CD950143
EST:     GATCCTGGCATCG                         ATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA
genomic: GATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCA

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: 46 (upstream exon), 45 (downstream exon)
Score: 11

GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCATTGGGCTCACGACCATATTCGGCAACGTCGACACAGAAGGCGCAACATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 62

GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCATTGGGCTCACGACCATATTCGGCAACGTCGACACAGAAGGCGCAACATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCATTGGGCTCACGACCATATTCGGCAACGTCGACACAGAAGGCGCAACATG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 31

GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcc ... ctatttctagATGATAGCATGGCTATCCTAATGGCGTTCAGAGCACATACTCTGGAAATCATTGGGCTCACGACCATATTCGGCAACGTCGACACAGAAGGCGCAACATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTGTTCTTCAGTGGAGGCGCCGGCCGGACTCGCGATGGAGCGGGACGGCCAGCAGACCCGCCGCGACAAGCTCATCATCGATACGGATCCCGGCATCGgttcgtctcccgtccctctcatttcctcctccgcgttgtcattgtttcgtttctttaaagctccatataactagttttcgtgtattcgacctcgaaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgtccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccgc