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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacaactgcttacaaccttgaacttcgattattgtgataaaaacatcgagtgttgtttatggagatgtaacatgcatgctgatttactgtcaatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC

Basic information

species Zea mays
transcript GRMZM2G139533_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139533_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g11050.1 (Oryza sativa), 3'ss of exon 7
gacaactgcttacaaccttgaacttcgattattgtgataaaaacatcgagtgttgtttatggagatgta-acatgcatgctgatttactgtcaattta----cagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC
    ||  |   |    | | ||||  ||| ||  ||||  ||  |      || |||||||| ||  | |    |||||  || |||||| |||| |    ||||| ||||| ||||||||||||||||||||||| || ||| |||| ||||| |||||||||||||||||||| |||||  |||||||    |||  | |||
---taccaccatctctttggcactt--atttttaagatagtaattttcgtaattatttatggacataaagaagctcatgccaatatactgttaattgatttccagGGTTCCAGGCTTACAGCTTTCGAGTTAGTTCACGACAAAGTACCCGCAACGCTGATAGCAGATTCTGCTGCAGCTGCACTGATGAAGAGCGGGTGTATTC

upper sequence: GRMZM2G139533_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 6
gacaactgcttacaaccttgaacttcgatt-attgtg-ataaaaacatcgagtgttgtttatggagatgtaacatgcatgctgatt-tactgtcaatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC-
   | |||  |  |   |   | ||| ||| | ||   |  |  | ||| |   | | ||     |  |     ||| | |  ||  || |||  | || |||||||| |||||||| || || ||||| || |||||||||||||| | ||| || || || ||||||||||  | |   |||     ||| | | ||| |  
---atctgtgttaagaatgacatttccattgactgcacactatgaaatcaaagttagattgatttggaggtttttgcttaccaatcataatgtttaattgcagGGATCTAGACTTACTGCCTTTGAGTTGGTGCATGAAAAAATACCAGGAACTCTTATTGCCGATTCTGCTGACGGT-TATTGGCCGGACATGTGGATGCTGT

upper sequence: GRMZM2G139533_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g00830.t01 (Vitis vinifera), 3'ss of exon 7
--gacaactgcttacaaccttgaacttcgattattgtgataaaaacatcgagtgttgtttatggagatgtaacatgcatgctgatttactgtcaatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC
     |   | ||| |   |  |   |  | |  |  | ||     ||  |   | ||  |   | || |    | | |  || ||   |  | |  | ||||||||||| ||||||||||| ||||| || ||||| || |||||||| || || |||||||| |||||||| ||||| || ||| |    || |  ||  
attgaagtggtttatattataaatggttaagttgtaggttatttttatataacatggt--acttaaatttgcttttctttttgtttctttaaccaactgcagGGATCCAGGCTTACAGCTTTTGAGTTGGTGCATGATAATATACCTGCTACTCTTATAGCAGACTCTGCTGCAGCTGCATTAATGCAGGCTGGACGCGTGG

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|76017068|gb|DT944238.1|DT944238
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|78084278|gb|DV512671.1|DV512671
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|60359093|gb|DN226066.1|DN226066
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|78116800|gb|DV535187.1|DV535187
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|37398320|gb|CF636472.1|CF636472
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|71445094|gb|DR826144.1|DR826144
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|74244684|gb|DT652598.1|DT652598
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|60352019|gb|DN218992.1|DN218992
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|71435544|gb|DR816594.1|DR816594
EST:     GGGGAGGTTTAGAGGAGGCCTTTTGCACCGAAACTCGTCCATT-AACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAA
EST: gi|78091338|gb|DV519712.1|DV519712
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|76921923|gb|DV168769.1|DV168769
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|78180539|gb|DV551032.1|DV551032
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|76285911|gb|DV025479.1|DV025479
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|67021902|gb|CO450651.1|CO450651
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|88749182|gb|DY533323.1|DY533323
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|6964770|gb|AW433463.1|AW433463
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGNCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|74242198|gb|DT650112.1|DT650112
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|60347352|gb|DN214325.1|DN214325
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCT
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCT
EST: gi|74233420|gb|DT641334.1|DT641334
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTTAGT-CATGAAAAAATACCTGCCAC
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTT-AGTTCATGAAAAAATACCTGCAAC
EST: gi|71756819|gb|DR954756.1|DR954756
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCA-TTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|74233419|gb|DT641333.1|DT641333
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|71445095|gb|DR826145.1|DR826145
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACA
EST: gi|71427098|gb|DR808148.1|DR808148
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAGCTTTCGAGTTAGTTCATGNNNNNNNTACCTGCAAC
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAA-TACCTGCAAC
EST: gi|32856195|gb|CD995876.1|CD995876
EST:     GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAG                         GGATCCAGACTTACAG
genomic: GGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 222

AACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 343

AACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

AACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

AACTGCTGGTTATGGAACTGCCCTTGGGGTTATACGCGCTCTTCATTCGGGGGGAGTTTTAGAGAAGGCCTTTTGCACCGAAACTCGTCCATTTAACCAGgttgatactc ... caatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgagtgttgtttatggagatgtaacatgcatgctgatttactgtcaatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC
                               tgctgat  putative branch site (score: 169)
       ttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacaactgcttacaaccttgaacttcgattattgtgataaaaacatcgagtgttgtttatggagatgtaacatgcatgctgatttactgtcaatttacagGGATCCAGACTTACAGCTTTCGAGTTAGTTCATGAAAAAATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC