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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcaatcagtcgcatttctgcaaattttttttttaaaaatagcttcagctatgatttcaatgagttcaactaacaaaattggtctgcatgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG

Basic information

species Zea mays
transcript GRMZM2G161019_T04
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161019_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g41120.2 (Oryza sativa), 3'ss of exon 10
tctgcaatcagtcgcatttctgcaaattttttttttaaaaatagcttcagctatgatttcaatgagttcaactaacaaaa--ttggtctgcatg--atcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG
   | |||  |     ||| |  |  |   | | | | || ||   | ||| |    |   |||  | ||| | || |||  || |||||| |   ||||||||| || |||||||| || || |||||||||||||||||||| || || |||||||| |||||||| ||||||||| ||||||| ||||||||||  || ||
-aaggaattggctctgtttatctatgtgcctgtgt-ataagtaatgt-agcaa-acctagtatggatgcaagtcactaaacttttgtctgccttgtatcctcagGGGTTTTCACCGTCTCCGGCATCATTGACTCGTTCATATATCACGGGCAGAAGGCACTCAAGAAAAAAATGGAGCTAGGCAAGTACAGATGATTTACCTG
















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|94476603|gb|EB705561.1|EB705561
EST:     TAGATTCCCCTACTCCACTACCTGACAAACCCTTTGTGCTATAGTGGGAG                         GTGTGTTCACCGTTTCTGGTATCATTGAATCGTTCATATACCAGGGACAGA
genomic: TAGAT-CCC-TACTCCACTACCTGACAAACC-TTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
EST: gi|32795051|gb|CD947287.1|CD947287
EST:     GATCCCTACT-CA-TACCTGAC-AACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
genomic: GATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
EST: gi|30088122|gb|CB886327.1|CB886327
EST:     AAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
genomic: AAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
EST: gi|32802331|gb|CD954567.1|CD954567
EST:     GATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
genomic: GATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
EST: gi|32804680|gb|CD956916.1|CD956916
EST:     GATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAG                         GTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA
genomic: GATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGA

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: 100

GTGATATTCACAGAAGAAAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 144

GTGATATTCACAGAAGAAAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GTGATATTCACAGAAGAAAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GTGATATTCACAGAAGAAAATAGATCCCTACTCCACTACCTGACAAACCTTTGTGCTATAGTGGGAGgtatgagcat ... tgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagctatgatttcaatgagttcaactaacaaaattggtctgcatgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG
                        aactaac  putative branch site (score: 150)
                                                tcctc  putative PPT
                           taacaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcaatcagtcgcatttctgcaaattttttttttaaaaatagcttcagctatgatttcaatgagttcaactaacaaaattggtctgcatgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
tctgcaa
- - - - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - -gcttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctgca