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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatcctttgtgctgattttggtttattgtgaacaaagaatggtctctgtaaaagattattaaggagtttgtcttctgaacttccaaacatgtta...

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 4
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatcctttgtgctgattttggtttattgtgaacaaagaatggtctctgtaaaagattattaag--gagtttgtcttctgaac--ttccaaac-atgtta-
|||||||| ||||||||||| || ||||||||||| |||||||||||||| |||||||| || |||||||||||||| || ||||| |||||||| ||||||||| |      ||| ||  |     | | ||| ||| |     |  |     ||  |   ||  |    |  | | | || | |||  ||||| || || | | 
ACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGAATGTTGGTGCAAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggc------tgtacttgtaccattctgttgagaatacttggtccttctgttagcattctacaactttggttatatattataaacaattccagaccatctcat

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 4
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatccttt--gtgctg-attttggtttattgtgaacaaagaatggtctctgtaaaagattattaaggagtttgtcttctgaacttccaaacatgtta
|| ||||| |||||||||||||| ||||| | ||| |||||| | ||||| || ||||| || |||||||||||||| |||||||||   ||||||||||||| |  ||  | |   | ||| ||| |  ||||||        || || | ||   |     |||| ||| |||  |    ||| |  |  ||         
ACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGAATATCGGTGCCAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGACGTGGCTGGTGATGgtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgtt-attaataatgagggtacaatctaatttggcag--------

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 4
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgta---tgacatcctttgtgctgattttggtttattgtgaacaaagaatggtctctgtaaaagattattaaggagtttgtcttctgaacttccaaaca--tgtta--
|||||||| |||||||||||||| ||||||| ||| |||||||||||||| || ||||| || |||||||| ||||| ||||||||    |||||||||||||   ||| ||       |  |||| || || || || |||      |  ||||| | |   | | ||      | |    |   |  || ||      |||||  
ACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGAATGTTGGTGCCAGTCTTGTAAAGCAGGTTGCAAATGCTACTAATGATGTGGCTGGTGATGgtaagctgatatatccaaagaagattgtgcttaatagtcaac------ttttctctattagttact-ttgttacttgtacaatactagattgcatgtggttgttaaa

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 4
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgta---tgacatcctttgtgctgattttggtttattgtgaacaaagaatggtctctgtaaaagattattaaggagt-ttgtcttctgaacttccaaacatgtta
|||||||| |||||||||||||| ||||||| ||| |||||||||||||| || ||||| || |||||||||||||| ||||||||    |||||||||||||   ||| ||       |  |||| |  || || || ||          |   |      | |  ||    | | ||   ||      ||||     |    
ACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGAATGTTGGTGCCAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGATGTGGCTGGTGATGgtaagctgatatatccaaagaagattgtacttcatagtaaatttttgtctattggttacttcgttacttgtacaatattagattgcatggttccgtggtt----

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 3
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatcctttgtgctgattttggtttattgtgaacaaaga-atggtctctgtaaaagattattaaggagtttgtcttctgaacttccaaacatgtta
|||||||| || || ||||| || || || | | | ||||| |||||||| || |||||||| |||||||| ||||| ||||||||   |||||||||||||| || ||  ||  |  |||||   | ||||   |  || ||   | |   || |  || | |||  |  | |   |  | | |  |  ||  ||     
ACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGAACGTTGGTGCTAGTCTTGTGAAGCAGGTTGCAAATGCTACTAATGATGTTGCTGGTGATGgtaagatat--ttcattttgatt---gattatgcggttcatagttgtagaaactttgcaaaactatgtaccaatgc-ttgtttaacttgtcatgcag----

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 4
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatcctttgtgctga-----------ttttggtttattgtgaacaaag--aatggtctc-tgtaaaagattattaaggagtttgtcttctgaacttccaaacatgtta------------
|||||||| ||||||||||| || ||||||||| | ||||| |||||||| || |||||||||||||||||||| || || ||||||   ||||||||||||| |   ||| ||    ||            ||||   || |||  ||    |    | ||||| | |  |    ||||||   || | | || |      | ||| || |              
ACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGAACGTTGGTGCCAGTCTTGTGAAACAGGTTGCTAACGCCACAAATGACGTAGCTGGTGATGgtaagtgttccctttcaatggattaaaacgttttttctgtttttgctaattgggttgttagtctcctatctactcatattaatcggtgt-ttttgtatctgacaaaatatatggtatgcgttacag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 4
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatcctttgtgctgattttggtt-tattgtgaacaaagaatggtctctgtaaaagattattaaggagtttgtcttctg-aacttccaaacatgtta-
|||||||| || |||||||| || |||||| || | |||||||||||||| |||||||||||||||||||| ||||| ||||||||    || || ||||||| |   || | |||    | ||| ||  |  | | || |  |  ||     | ||     ||  |||    |   ||||||| || |     |   |||| 
ACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCAAATGCCACTAATGATGTAGCAGGAGATGgtaagttttcatctgttgcaactttagtggttctattaaaatggtttgaagattcta---ttttgataattgatgcatcttctgcaaatgatttaatggttaa

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|91054374|gb|EB164792.1|EB164792
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|71758555|gb|DR956492.1|DR956492
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|149073906|gb|EE162234.2|EE162234
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|78078492|gb|DV506905.1|DV506905
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|211348396|gb|FL389757.1|FL389757
EST:     AGCCCTTGTGAA-CAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTAC-ACATGTGCTACTGTTTTGACAAAAGCA-TATTTACTGAGGGGTGCG
genomic: AGCC-TTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|67019174|gb|CO447923.1|CO447923
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACCAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACGAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|149077207|gb|EE165873.2|EE165873
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|19770413|gb|BQ035134.1|BQ035134
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACCAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACGAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|71425565|gb|DR806757.1|DR806757
EST:     GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATG                         GTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: GAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA

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: 317

ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 181

ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatc ... aaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCGAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGTGATGgtatgacatcctttgtgctgattttggtttattgtgaacaaagaatggtctctgtaaaagattattaaggagtttgtcttctgaacttccaaacatgtta

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