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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcctttctctttcgatccgacccccgcttgccttgcctctacgcatgcctaactcgcgggattattaataaaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG

Basic information

species Zea mays
transcript GRMZM2G422649_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G422649_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g63590.1 (Oryza sativa), 3'ss of exon 2
---------------------gtaatctcctttctctttcgatccgacccccgcttgccttgcctctacgcatgcctaactcgcgggattattaataaaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
                      |     ||||| |||||   |       || |||   |    |||  || |  ||  ||       |      ||||| || ||||||||||||||||||||| ||||| ||||| |||||||||||||||
gtacttattccccccactctcttttcaccctttttcttttattttctttgccccttctgtcaaatctgtgcgtctcttgctta--acttcgcccttaaaatttgcagCTTTCACTTGGACCATGCTGCCTCTCTTCCCTACTTCTTGGAGAAG
















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|91876870|gb|EB406827.1|EB406827
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|31350152|gb|CD434509.1|CD434509
EST:     TACTTCGACGAGATCGACCCATCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|211185208|gb|FL070464.1|FL070464
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|149077596|gb|EE166295.2|EE166295
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|148945486|gb|EC890724.2|EC890724
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|50337754|gb|CO532880.1|CO532880
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|20301206|gb|BQ164149.1|BQ164149
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|149060216|gb|EE157191.2|EE157191
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|211185207|gb|FL070463.1|FL070463
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|89252160|gb|DY623946.1|DY623946
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCCTCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCTTATTTCTTGGA-AAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|78077825|gb|DV506254.1|DV506254
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|71768944|gb|DR966881.1|DR966881
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
EST: gi|28909464|gb|CB331825.1|CB331825
EST:     TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA                         CTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
genomic: TACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG

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: 48 (upstream exon), 46 (downstream exon)
Score: 133

TTCGACTGCGGCATCCACCCCGCGTACTCCGGCATGGCGGCGCTGCCCTACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG


Block sizes: 43 (upstream exon), 40 (downstream exon)
Score: 11

TTCGACTGCGGCATCCACCCCGCGTACTCCGGCATGGCGGCGCTGCCCTACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 18

TTCGACTGCGGCATCCACCCCGCGTACTCCGGCATGGCGGCGCTGCCCTACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG


Block sizes: 33 (upstream exon), 46 (downstream exon)
Score: 21

TTCGACTGCGGCATCCACCCCGCGTACTCCGGCATGGCGGCGCTGCCCTACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCAgtaatctcct ... aaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgccttgcctctacgcatgcctaactcgcgggattattaataaaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG
                                     tattaat  putative branch site (score: 21)
                                   attattaataaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcctttctctttcgatccgacccccgcttgccttgcctctacgcatgcctaactcgcgggattattaataaaaattacagCTTTCACTTGGACCATGCCGCCTCGCTTCCGTACTTCTTGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA