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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcctaaatctcctacgcgttgcacatttcctaagttcttatcgcattgcctcctccaatgggaagtttagtgtgtgttccggcattgcggggat...

Basic information

species Zea mays
transcript GRMZM2G101217_T08
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 5'ss of exon 2
GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcctaaatctcctacgcgttgcacatttcctaagttcttatcgcattgcctcctccaatgggaagtttagtgtgtg--ttccggcattgcggggat----
|||||||| ||| ||||||||||||||||||||||||||||||||||| ||||||| |||||||| || ||| ||||||||||||||||||||||||| |||  ||  |       ||| |   ||| |   |||    | |   | || |||      |  |   || ||||| |||||||  ||||||||||||||| ||    
GTGAGGTCGGCGCTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGTCGGGACCCGTGGGCGTGCTCGACTCCAGCATCCGCTTCAACCAGCTCGACGgtaatcctcctttctacctgcttcttggatcattctattgcttggaccggatt------tggatgtgggagtttggtgtgtgtgttccggcattgcgggaatcaga
















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|148960597|gb|EE011219.2|EE011219
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|101391071|gb|EB817469.1|EB817469
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211428747|gb|FL388358.1|FL388358
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATR
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGAT-
EST: gi|89250708|gb|DY622494.1|DY622494
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTTGATAAGCTGTATAAGAAGCATGAT
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTT-GATAAGCTGTATAAGAAGCATGAT
EST: gi|19436955|gb|BM953365.1|BM953365
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211269212|gb|FL410574.1|FL410574
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211085712|gb|FL420035.1|FL420035
EST:     GGGGCCGGTGGGCGTTCTTGACG-CAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|37417541|gb|CF646424.1|CF646424
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71327533|gb|DR800378.1|DR800378
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71418854|gb|DR804568.1|DR804568
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|50336106|gb|CO531232.1|CO531232
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211153475|gb|FL406036.1|FL406036
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211197467|gb|FL425782.1|FL425782
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|50325602|gb|CO520728.1|CO520728
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71312573|gb|DR792811.1|DR792811
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211164475|gb|FL391064.1|FL391064
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGANGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211524044|gb|FL387968.1|FL387968
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|93012306|gb|EB637826.1|EB637826
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|76924073|gb|DV169790.1|DV169790
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|93012540|gb|EB638060.1|EB638060
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211531113|gb|FL426903.1|FL426903
EST:     GGGGCCGGTGGGCGTTCTTGACGC-AGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71303088|gb|DR787655.1|DR787655
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211491486|gb|FL425979.1|FL425979
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211209580|gb|FL394645.1|FL394645
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA

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), 48 (downstream exon)
Score: 75

GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 17

GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 22

GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 38

GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAGGTCAGCGTTGTACGACCCCAACCATGGCTACTTCTCCAAGCGGGCGGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcctaaatctcctacgcgttgcacatttcctaagttcttatcgcattgcctcctccaatgggaagtttagtgtgtgttccggcattgcggggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC