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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacgtacgcgtgcaaagtgatgcctcgatctagctcaagtcgttccaggagattgtagaaccatatatcctgagacgacgacgacagtacgtgttgcattgcagtacatactgatatactgcgcgcgttgtggtgtgtttgcatcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG

Basic information

species Zea mays
transcript GRMZM2G025954_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025954_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g68480.1 (Oryza sativa), 3'ss of exon 1
------------------------------gtacgtacgtacgcgtgcaaagtgatg--cctcgatctagctcaagtcgttccaggagattgt-agaaccatatatcctgagacga-cgacgacagtacgtgttgcattgcagtacatactgatatactgcgcgc--gttgtggtg-tgtttgcatca--tgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG
                               |   | ||      |    | |||||  |      || ||   | |  |||      ||    ||    || |||  ||| | || || ||  | || |    | |    |   ||| |   |   | | |       |||     ||  ||  | |  ||||||||||| |||||||| |||||||| || || ||||||||||||||||||||| ||| |||||| ||||||||||| || |||||||| || |||||||||
gtacttcacaaaagccacaaaactccactgatctcttcgcgtcaatctccattgatgaactgttgcctcgcatgaattcttcagtcttatcacgagctggatttattttgaaatgagcggcgtgaataagaaagggaacagatctcatcccactgctcagtgtaataactgtaaaactgactggttgatttgcagGTGCGGCCCTTGCAAGGTGATGGCACCGAAATTCCAGGAGATGTCCGAGAAGGACCAGGACGTTGTGTTCCTCAAACTCGACTGCAATCAAGACAACAAG

upper sequence: GRMZM2G025954_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G16400.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgtacgtacgcgtgcaaagtgatgcctcgatctagctcaagtcgttccaggagattgtagaaccatatatcctgagacgacgacgacagtacgtgttgcattgcagtacatactgatatactgcgcgcgttgtggtgtgtttgcatcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG
                                          | | | |  ||  || | ||  |  | || | |||    |  |  || |  |    |    ||||        ||  | |  | |   | | ||      || ||    |||||||| || |||||||||||||| |||||||| | | | ||| | || |||||| ||| |||| | ||||| || ||||| || || ||||| |||||||||
----------------------------------------tgaat-gcttgagatgagtttactattaaatgttctgttttggtgttgagaaaa---atcagtttgc------ctctcttttttttcaatcctcgt------ttggctctttgcagGTGTGGTCCTTGCAAAGTGATTGCTCCCAAATACAAAGAGCTATCGGAGAAGTACCAGGACATGGTGTTTCTTAAGCTTGATTGTAACCAAGACAACAAG

upper sequence: GRMZM2G025954_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0023g00740.t01 (Vitis vinifera), 3'ss of exon 1
gtacgtacgtacgcgtgcaaagtgatgcctcgatctagctcaagtcgttccaggagattgtagaaccatatatcctgagacgacgacgacagtacgtgttgcattgcagtacatactgatatactgcgcgcgttgtggtgtgtttgcatcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG
                                                  || ||  |   |   | |  | |  ||  ||      |    | |   ||   |||  |||||   | || |||     |   | | || || ||  ||  | |||||| || || ||||||||||||||||| || ||||| ||  |||| | |||| | || ||||| || || || ||||||||||||||||| |||||||||
--------------------------------------------------caagaactgccaatgcgacttgtaatgcaactcatctgttgatccaattttttttg--gtaca---ttatttacctgatgtcatattgt-tgcttaaattcttcagGTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAG

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|32841806|gb|CD981487.1|CD981487
EST:     GTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|91873796|gb|EB403753.1|EB403753
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|6952325|gb|AW424393.1|AW424393
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|211391451|gb|FL111189.1|FL111189
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|6195037|gb|AW147141.1|AW147141
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|15632285|gb|BI679378.1|BI679378
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGT
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGT
EST: gi|149096373|gb|EE182103.2|EE182103
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|211391453|gb|FL111191.1|FL111191
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|16379905|gb|BI993210.1|BI993210
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|148947826|gb|EC893315.2|EC893315
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|148947825|gb|EC893314.2|EC893314
EST:     GTCGAGGCCGCCGGCGACAAGGTGGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTCGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|211423528|gb|FL160044.1|FL160044
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAG
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAG
EST: gi|211391452|gb|FL111190.1|FL111190
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGGCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|13491074|gb|BG517838.1|BG517838
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|6166617|gb|AW144881.1|AW144881
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGCCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|148991280|gb|EE032751.2|EE032751
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|16379812|gb|BI993161.1|BI993161
EST:     CTCGACATGTACCCCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: CTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|6166616|gb|AW144880.1|AW144880
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|148930342|gb|EE284761.2|EE284761
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
EST: gi|211256127|gb|FL475672.1|FL475672
EST:     GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATG                         GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA
genomic: GTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAA

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 24

CCGTCACCGGGCAGGTCACGGAGGTCAACAAGGACACCTTCTGGCCCATCGTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

CCGTCACCGGGCAGGTCACGGAGGTCAACAAGGACACCTTCTGGCCCATCGTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 42

CCGTCACCGGGCAGGTCACGGAGGTCAACAAGGACACCTTCTGGCCCATCGTCGAGGCCGCCGGCGACAAGGTCGTCGTCCTCGACATGTACACCGAATGgtacgtacgt ... catcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgcagtacatactgatatactgcgcgcgttgtggtgtgtttgcatcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG
            tactgat  putative branch site (score: 42)
               tgatata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacgtacgcgtgcaaagtgatgcctcgatctagctcaagtcgttccaggagattgtagaaccatatatcctgagacgacgacgacagtacgtgttgcattgcagtacatactgatatactgcgcgcgttgtggtgtgtttgcatcatgcagGTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA