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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatctactaatgatagtctagcctttaaaatttctatgtggcggttcttgtttctaaatgcataggctacccatttcttaccacaatttctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA

Basic information

species Zea mays
transcript GRMZM2G084881_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084881_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 3'ss of exon 3
acaatctactaatgatagtctagcctttaaaatttcta----tgtggcggttcttgtttctaaatgcata-----ggctacccatttcttaccacaatttctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA
         || |  || | |  |||||  || ||||     | || |  || ||  ||     | ||        ||      ||||||| || || |||| |  |||||||||||||| ||||| ||||| || ||||| || ||||||||||||  ||
---------tagtcctaatttgccctttgcaagttctgtcattctgtcaatttttacttgcttgttcaccaacacagcattgtgtttcttatcaaaagttctctttcagGTGGCTCCTTATGAGCGCCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA
















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|32925307|gb|CF030119.1|CF030119
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATTATCTCCAAGGAGGCT                         GTGGCTCCTTACGAGCGTCCTGCCCCAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|87153386|gb|DY398175.1|DY398175
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTATGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|4321049|gb|AI467712.1|AI467712
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|211319160|gb|FL268453.1|FL268453
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|32926982|gb|CF031794.1|CF031794
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTCCGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTCCG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|4314900|gb|AI444697.2|AI444697
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|67018255|gb|CO447004.1|CO447004
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
EST: gi|32846014|gb|CD985695.1|CD985695
EST:     CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCT                         GTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG
genomic: CCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACG

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: 280

GGGTACGCGGCGCGGGAGTTCGCCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1027

GGGTACGCGGCGCGGGAGTTCGCCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 814

GGGTACGCGGCGCGGGAGTTCGCCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1237

GGGTACGCGGCGCGGGAGTTCGCCAAGCAGGGAGTTAAGCCTGGGGAGCTTGCAATCATCTCCAAGGAGGCTgtatgtttct ... tctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttgtttctaaatgcataggctacccatttcttaccacaatttctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA
                               ttcttac  putative branch site (score: 1237)
                                           tttcttt  putative PPT
       tttctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatctactaatgatagtctagcctttaaaatttctatgtggcggttcttgtttctaaatgcataggctacccatttcttaccacaatttctttgacagGTGGCTCCTTACGAGCGTCCTGCCCTAAGCAAAGGTTACCTCTTTCCTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - -ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accacaa