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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_T01
intron # 12
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagctatgatttcaatgagttcaactaacaaaattggtctgcatgatcctcagGTGTGTTCACCGTTTCTGGTATCATTGACTCGTTCATATACCATGGACAGAAGGCGCTCAAGAAGAAAATGGAGTTAGGCAAATACAGATGATCAACTTG
                        aactaac  putative branch site (score: 1)
                                                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