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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttcttgctctcagaacatacgctaatctatatatgcatacatatgcttcatttggctctatgacggtaagcttaaaatgtctcaaaatgtgttgtttacag

Basic information

species Zea mays
transcript GRMZM5G826979_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G826979_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g03190.1 (Oryza sativa), 5'ss of exon 5
CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttcttgct-ctcag-aacatacgctaatctatatatgcatacatatgcttcatttggctctatgacggtaagcttaaaatgtctcaaaa--tgtgttgtttacag
||||||||| || ||||| ||||| ||||| || || ||||||||||||||||| ||  ||||||| || || || || |||||||||||||||||||||||     |   |||| ||||   ||| | || ||||| ||          | ||  ||| |   |   |       | ||||||||||| || |||  | |||  | | |||
CAGCACTCAGTCTAAGGAACAAATTGAGGCGAGTCTTATAAGCAGGCAAGAGGCTGCAGTAAGAAGGGAGAGGGCGCTCGCATATGCATTTTCACATCAGgtagatatctgtgcttctcaatgacagatgccaatctgtac---------tctgactcactcaaccacac------atgcttaaaatgtttcgaaacttctgtcttctgcag

upper sequence: GRMZM5G826979_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0040g02360.t01 (Vitis vinifera), 5'ss of exon 5
CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttcttgctctcagaacatacgctaatctatatatgcatacatatgcttcatttggctctatgacggtaagcttaaaatgtctcaaaatgtgttgtttacag--------------------------------------------------------------------------------------
||||   ||||| || || ||||| || ||| ||||| ||| || ||||| |||||| || ||||||||||| || || || ||||||||||| ||||||||     | ||     |||  ||     |    | || ||| |||   || | |  |     |||  ||   | |   |  |  | |||    |||   ||   | |                                                                                       
CAGCCTACAATCAAAAGAACAAATTGAAGCAGGCCTATTAAACAAGCAAGGGGCAGCAATGAGAAGAGAAAGGGCACTGGCTTATGCATTTTCTCATCAGgt----atcctattcatcaatactgtttcctgcccat-tatccatttttaggatcaa--gaactcactggttggatcttccagttatcttggtatgaaatggaaagaaaatcaaataccagtggtgcactcatgtagacacatgttttattattgcaaattcttgattaatccctgatggaattggtcctacag
















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|5566899|gb|AI881810.1|AI881810
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|7162438|gb|AW520060.1|AW520060
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|74235105|gb|DT643019.1|DT643019
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|211476335|gb|FL157892.1|FL157892
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         NGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTG
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTG
EST: gi|76286750|gb|DV026318.1|DV026318
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|78118474|gb|DV536859.1|DV536859
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|149086412|gb|EE175954.2|EE175954
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCCATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|78083867|gb|DV512260.1|DV512260
EST:     GGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTTC-CATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCCAATAA
genomic: GGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTT-CACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAA
EST: gi|71303411|gb|DR787813.1|DR787813
EST:     AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
genomic: AGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC
EST: gi|6626384|gb|AW257916.1|AW257916
EST:     GCTCTTGCATATGCATTTTCACATCAG                         TGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAAAAAC
genomic: GCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAAC

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), 46 (downstream exon)
Score: 62

CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAACTTGCAGTGGGGCTGGAGCTGGTTGGAGCGCTGGATGGCAGCAAAACCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAACTTGCAGTGGGGCTGGAGCTGGTTGGAGCGCTGGATGGCAGCAAAACCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 41

CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAACTTGCAGTGGGGCTGGAGCTGGTTGGAGCGCTGGATGGCAGCAAAACCTT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 81

CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttc ... ttgtttacagTGGAAGAGCACATCAAGATCTGCGAACCCAATGTTTGTAGACCCAAATAACTTGCAGTGGGGCTGGAGCTGGTTGGAGCGCTGGATGGCAGCAAAACCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCACTCAATCCAAGGAGCAAATCGAGGCAAGCCTAATAAGCAGGCAAGAGGCAGCGATAAGAAGAGAAAGAGCTCTTGCATATGCATTTTCACATCAGgtttgagttcttgctctcagaacatacgctaatctatatatgcatacatatgcttcatttggctctatgacggtaagcttaaaatgtctcaaaatgtgttgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT