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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactgctcacagaattcctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG

Basic information

species Zea mays
transcript GRMZM2G077233_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 4
gtaaactgctcacagaatt-cctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG
|| |  |  || ||  |||  |||| | |||  ||   || ||||||||||  || |    || |   ||||  ||||||  || |||||||||||  | ||| | |||| |||||||||||| ||||||||||||||||||||||| || |||||||| || || ||||| |||||||
gtgactta-tcgcactattgtctcagtaaaacatttagatgcatcattgttgatgctgcaggt-ccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG
















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|6989633|gb|AW447846.1|AW447846
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATT-ATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTG
EST: gi|211504863|gb|FL422036.1|FL422036
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGA
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGA
EST: gi|8367213|gb|BE050158.1|BE050158
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|76291015|gb|DV030583.1|DV030583
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211068181|gb|FL270394.1|FL270394
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAAC-AGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211373714|gb|FL377783.1|FL377783
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|76289740|gb|DV029308.1|DV029308
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|60357617|gb|DN224590.1|DN224590
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCGGCCCTACTTTTC-TCATTGGGAA
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTT-CATCATTGGGAA
EST: gi|101393193|gb|EB818527.1|EB818527
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|32851441|gb|CD991122.1|CD991122
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211384115|gb|FL248478.1|FL248478
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|67034446|gb|CO462996.1|CO462996
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|91876413|gb|EB406370.1|EB406370
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGGGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGGAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG

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: 388

GAGAATCTTGTACGATAACATATGGTTCTGGGCAAATCGCTGGCTTCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 500

GAGAATCTTGTACGATAACATATGGTTCTGGGCAAATCGCTGGCTTCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 576

GAGAATCTTGTACGATAACATATGGTTCTGGGCAAATCGCTGGCTTCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 564

GAGAATCTTGTACGATAACATATGGTTCTGGGCAAATCGCTGGCTTCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG
                                           ctttttgttc  CT-rich tract
                               ataatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactgctcacagaattcctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG