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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttatccttgaatttgctgtatccacatgaagcccttggttaatttgacttcttattacggatctgatgataaatcacttggtcgttatattgtt...

Basic information

species Zea mays
transcript GRMZM2G090904_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 1
GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttatccttgaatttgctgt-atccacatgaagcccttggttaatttgacttcttattacggatctgatgataaatcacttggtcgttatattgtt----
||| || ||||| || || || ||||||||||||||||| ||||| ||||||||||||||  || | ||||| ||||||||||||||||||||||| |  || |||||     || ||||  | | |||| | |||| || |  ||| ||||  ||     ||   ||||||    ||||   |   ||   ||  |  ||    
GCACCGCCACTCGAATGCGCTCGTCGACGTGCTGCCGCCCGAGGCGGACTCCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttctgctggattttttctgatccgcgtgaa-ccttatgttgatttatct----gttctagatctgcctgtaaagtgccatgtttctagttaatttaat

upper sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G31450.1 (Glycine max), 5'ss of exon 1
GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttatccttgaatttgctgtatccac-atgaagcccttggttaatttgacttcttattacggatctgatgataaatcacttggtcgttatattgtt
 || || ||||||||||| || |||||||| || || |||||||||||||||||||||||  |  |  |   ||| ||||||||  |||||||||| || || ||||| |    |  |||| ||| | | | ||  |    | |||||   || |     || |    |  | |  |   ||   || | |||   ||   
CCACCGCCACTCCAACGCCCTCGTCGACGTTCTTCCACCGGAGGCCGACTCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAATgtcagtttctatacgt-tttgttgttttccctatcgaattttaggttaccgtggcgaaagatgatttctagggttttcgttctagtgctggtttggttagg

upper sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G31470.1 (Glycine max), 5'ss of exon 1
GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttatccttgaatttgctgtatccac-atgaagcccttggttaatttgacttcttattacggatctgatgataaatcacttggtcgttatattgtt
 || || ||||||||||| || ||||| ||||||||||||||||||||||||||||||||  |  |  |   ||| ||||||||  |||||||||| || ||  ||||    |  | |||| ||| |   | ||  |    | |||||   || |   | || |    |  | |   |  ||  ||  | |   | |  ||
CCACCGCCACTCCAACGCGCTCGTCGAGGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAATgtcggttt-cgttacattttgttgtttttcctatcgaattttaggttaccgtggcgaatgatgatttttagggttcaatttcttttaattgcagtttgatt

upper sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 1
-GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttatccttgaatttgctgtatccacatgaagcccttggttaatttgacttcttatta-cggatctgatgataaatcacttggtcgttatattgtt--------
  || || ||||||||||| || |||||||| || ||||||||||||||||||||||||||  |  |  |   ||| ||||||||  |||||||||| || || |||||          || | ||  | | |         | |    ||| | |||  |  | |   |||  || |   | | ||  |  |  | ||| |        
TCCACCGCCACTCCAACGCGCTCGTCGACGTTCTTCCGCCGGAGGCCGACTCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAtgtcagtttcg--------ttaccgtggcgaaagatcatttctag--ggttttatttcccacaatcatgtctagtgctggtttagtttcttttagtgttgattggcaatt

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|149106687|gb|EE188583.2|EE188583
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|50333575|gb|CO528701.1|CO528701
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|19437228|gb|BM953638.1|BM953638
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|71447068|gb|DR828118.1|DR828118
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|149077094|gb|EE165751.2|EE165751
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|149087906|gb|EE177166.2|EE177166
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|211369250|gb|FL299603.1|FL299603
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         C
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcag-
EST: gi|211369250|gb|FL299603.1|FL299603
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         C
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcag-
EST: gi|31664274|gb|CD572999.1|CD572999
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|32847684|gb|CD987365.1|CD987365
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|148931425|gb|EC874380.2|EC874380
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|71448676|gb|DR829726.1|DR829726
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|5915467|gb|AW053108.1|AW053108
EST:     GGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: GGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|149044685|gb|EE047658.2|EE047658
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|148937644|gb|EC881837.2|EC881837
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|19822279|gb|BQ048303.1|BQ048303
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGA
EST: gi|149097661|gb|EE183560.2|EE183560
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|5296120|gb|AI782995.1|AI782995
EST:     ACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: ACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|31998286|gb|CD662014.1|CD662014
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|32837207|gb|CD976885.1|CD976885
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|22521568|gb|BU080379.1|BU080379
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|76936161|gb|DV174612.1|DV174612
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCA
EST: gi|149001308|gb|EE038593.2|EE038593
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|6022605|gb|AW067417.1|AW067417
EST:     ACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAGAAGCAAGAAATACGGGAGGCGGNTGAA
genomic: ACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|19437001|gb|BM953411.1|BM953411
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGC
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGC
EST: gi|148970781|gb|EE021533.2|EE021533
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
EST: gi|148987102|gb|EE030930.2|EE030930
EST:     CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAAC                         GATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA
genomic: CCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAA

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: 256

GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 299

GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 279

GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCGTCACTCCAACGCTCTAGTCGACGTGCTGCCGCCGGAGGCCGACTCCAGCATCTCCTTGTTGGGATCGTCGGAGAAGCCCAACGTCACTTACAACgtaagtttatccttgaatttgctgtatccacatgaagcccttggttaatttgacttcttattacggatctgatgataaatcacttggtcgttatattgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC