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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgccggtaccattttctcatgctgttttatctaactgctccaagctattagctgttgcaaaactcttgcataatggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG

Basic information

species Zea mays
transcript GRMZM2G407044_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
tgatgccggtaccattttctcatgctgttttatctaactgctccaagct-att--agctgttgcaaaactcttgcataatggagggatcattgatgat-tgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
   ||   ||     |    ||     | | || ||     |  | ||  |||  |  | |||    |||  |||||| | ||    |    |    | ||||||||||||| ||||| ||||||||||||||| |||||||| | |||||||| |||||||||||||||
---tgaatgtttagctgaaccacaac-tgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG

upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 10
tgatgccggtaccattttctcatgctgttttatctaactgctccaagct-att--agctgttgcaaaactcttgcataatggagggatcattgatgat-tgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG----------------------------------
   ||   ||     |    ||     | | || ||     |  | ||  |||  |  | |||    |||  |||||| | ||    |    |    | ||||||||||||| ||||| ||||||||||||||| |||||||| | |||||||| |||||||||||||||                                  
---tgaatgtttagctgaaccacaac-tgtcatttactcatttaatgcccattcaaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGGTATATTGAATTCTTTTTGTACTTTTCTTTCACC

upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 10
tgatgccggtaccattttctcatgctgttttatctaactgctccaagctattagctgttgcaaaactcttgcataatggagggatcattgatgattg---cagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
  | |    | | | |||       ||| |   || |   || ||   |   || |  |  |  | | |||  |  |       |  |      |||   ||||||||||||||| | ||||||||||||||| |||| || || || || ||||||||||| ||||||
-aaagtatttgctagttt--tgaaatgtctgccctgatgacttcagattgacagatcctttattatttttgatttttaactaattggtatgcttttgaaccagCTTACTGGAGATTTGGACAAGATGGTTGCATTACAGAGATTGTTAGAACCATATGGCATTTGTGAG

upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 10
tgatgccggtaccattttctcatgctgttttatctaactgctccaagctattagctgttgcaaaactcttgcataatggagggatcat-tgatgattg--cagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
  | |    | | | |||       ||| |    | |   || ||   |   || |  | ||  | | |    |  |       | || ||||  |    ||||||||||||||| | ||||||||||||||| | || || || || || ||||||||||| ||||||
-aaagtatttgctagttt--ggaaatgtctgccatgatgacttcagattggcagatccttcattattttcaatttttatctaattgatatgatcttgaaccagCTTACTGGAGATTTGGACAAGATGGTTGCATTGCAGAGATTGTTAGAACCATATGGCATTTGTGAG

upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
----------tgatgccggtaccattttctcatgctgttttatctaactgctccaagctattagctgttgcaaaactcttgcataatggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
          ||| || |       |||  |||  |  |   ||||  |  |    ||| ||   ||||    |  |  |||  ||   |    |      ||  |  |||||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||| || ||||||
aaaaaatatatgaagctgacttggattttccatcttaatc--tctattttttt---gcttttg--tgttttggattttgtgctgaa---atttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG

upper sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv00s0220g00110.t01 (Vitis vinifera), 3'ss of exon 10
tgatgccggtaccattttctcatgctgtt-ttatctaactgctccaagctattagctgttgcaaaactcttgcataa--tggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
   | || |||   ||||||   | | |    |||       ||    ||      ||   |  |  |     |  |  |  ||  ||    | | ||| ||||| || |||||| |  |||||||||||||||| || |||||||||||||| ||||| || ||||||
-attacctgtat--ttttctggcgttttcaccatccctgcaatcttgccttcattttgcctcccagtttcactagcacttaaagctatttgcgtttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCCTATGGGATTTGTGAG

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|89253086|gb|DY624872.1|DY624872
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211452062|gb|FL278247.1|FL278247
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211122006|gb|FL444944.1|FL444944
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|24934868|gb|CA453086.1|CA453086
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|60338155|gb|DN205128.1|DN205128
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211132732|gb|FL016680.1|FL016680
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|149087823|gb|EE287139.2|EE287139
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211033398|gb|FL443777.1|FL443777
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|32940948|gb|CF045767.1|CF045767
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211350147|gb|FL469218.1|FL469218
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|116818053|gb|EC860984.1|EC860984
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211452063|gb|FL278248.1|FL278248
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|78122763|gb|DV541147.1|DV541147
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|60343820|gb|DN210793.1|DN210793
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|60340849|gb|DN207822.1|DN207822
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211449937|gb|FL278245.1|FL278245
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGG
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGG
EST: gi|24773364|gb|CA408618.1|CA408618
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211122005|gb|FL444943.1|FL444943
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCMCMCAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCMCTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|148949306|gb|EC894757.2|EC894757
EST:     TTTTCCGAGCAAAACCTGTTGATGTTTTTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211452064|gb|FL278249.1|FL278249
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
EST: gi|211132731|gb|FL016679.1|FL016679
EST:     TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA
genomic: TCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 114

GGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTGAAATCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

GGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTGAAATCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 20

GGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTGAAATCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GGTTTCTGTCAACACTGCTGCTCGGAAGGAAATCCTAGATATTGCTGAAATCTTCCGAGCAAAACCTGTTGATGTTTCTGACCACACAGTAACGCTTCAGgttggcatcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctattagctgttgcaaaactcttgcataatggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
                                        cattgat  putative branch site (score: 95)
                           ataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgccggtaccattttctcatgctgttttatctaactgctccaagctattagctgttgcaaaactcttgcataatggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
tgatgcc
- - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - -ctgctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttg