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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcatatattagaaaaaatatatttcactccctgctaatgatctttaccccttccag

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 5'ss of exon 8
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcata--tattagaaaaaatatatttcactccctgctaatgatctttaccccttccag-----------------------------------------------------
|||||| ||||||||||||||||| ||||||||| |||||||| | ||||||   | | |   |  ||  | | ||   |||   || |          ||||| | |    | ||    |                                                     
GACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTGgtaagacccttaccttctggtaactgtaaggttaaaatgatctagtataagattaatggtttgccacactattggttgcaaaattgcagatattccgtgcagtgctaacagtgtttgccccctttcag

upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA15G07480.1 (Glycine max), 5'ss of exon 9
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcatatattagaaaaaatatatttcactccctgctaatgatctttacccct--tccag-------------
|||||| ||||||||||| ||||| |||||||||||||||||||| ||||  | |   |  |    |     | |  |  | |  ||||    |    ||   |   ||  | |  | ||              
GACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTGgtaaattgactgttccgcttttatgcatatgagctttgcttcatattcaaacaaaatttactaatcatgattcactttgtgcttgcag

upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G31830.1 (Glycine max), 5'ss of exon 10
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcatatat-tagaaaaaatatatttcactccctgctaatgatctttaccccttccag-------------------
|||||| ||||||||||| ||||| |||||||||||||||||||| ||||  | |   |   | | | |||  | | || || |  |||||        ||  |  |||||   ||                       
GACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTGgtaaattgactgtt-ttgcttttatgcaaataagatttgcttcacatttca--aacaaaatttacttattattatttcactttgtgcttgcag

upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G25460.1 (Glycine max), 5'ss of exon 8
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcatatattagaaaaaatatatttca---ctccctg----ctaatgatctttaccccttccag------
|| ||||||||||||||| ||||| ||||||||| ||||||| || ||||    ||  | ||||  ||   |  | ||  |||  || |   ||    |    ||||| ||||| |   ||||         
GAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCATGTTTTATCTGgtaaatggattgt-actttttaatgtgcataagctatgcttaaaaactgtaagaaatctaatcatcttcatttcttctgcttacag

upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA07G31090.1 (Glycine max), 5'ss of exon 9
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcatatattagaaaaaatatatttca-----ctccctg----ctaatgatctttaccccttccag------
|| ||||||||||||||| ||||| ||||||||| ||||||| || ||||    ||  | |||| |||   |  | ||  | |  ||||     ||    |    ||||| ||||| |   ||||         
GAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCCTGTTTTATCTGgtaaatagattgt-actttataatgtgcataagctctgcttcaaaaaactgtaagaaatctaatcatcttgatttcttctgcttacag

upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 5'ss of exon 8
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatc--acttca-tatattagaaaaaatatatttcactccct----gctaatgatctttaccccttccag------------
|||||| |||||| ||||||||||||||||||||||    || || || || ||  |||     |||| |  | |      |||   ||| || |       | |     |   ||     |  |             
GACTGATAGTGCTCTGAAGTTTGGGTGGTTTTTCTTCACGTATCTGgtgagttttccatttggtttcagtgaactttttttaatggctttgacacatcaaaaggtggaagtgagtaaaagcttaaaatatgattgcag

upper sequence: GRMZM2G169773_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 8
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagat----tatcatcacttcatatattaga-----aaaaatatatttcactccctgctaatgatctttaccccttccag-----------------------
|||||| |||||| | ||||| ||||||||||||||||||||||| ||||| |    |||  ||  ||  |  ||  |      |     |   |  |    |||| |||  |  | ||| | |                           
GACTGATAGTGCTCTAAAGTTCGGGTGGTTTTTCTTGTTTTACCTGgtaagctgttttatgttctttttgtggatctggctttcacttgcaatgtagatgttctgcaaattgtggtcacctcattttttttgccttgttttctccatgcag

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|148980186|gb|EE026996.2|EE026996
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTTCTTGTTTTACCTT                         CTCCATATCTTATT
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTT-CTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATT
EST: gi|76293307|gb|DV032875.1|DV032875
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|88749197|gb|DY533338.1|DY533338
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|76293306|gb|DV032874.1|DV032874
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|71449251|gb|DR830301.1|DR830301
EST:     GACTGACAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|8368017|gb|BE050962.1|BE050962
EST:     GAAGTTTGGGTGGTTTTTCTTG-TTTATCTGT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATT
genomic: GAAGTTTGGGTGGTTTTTCTTGTTTTACCT-Tgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATT
EST: gi|78115059|gb|DV533447.1|DV533447
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTC-ATTT
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATT-
EST: gi|78115058|gb|DV533446.1|DV533446
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|78077114|gb|DV505548.1|DV505548
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|91049868|gb|EB160286.1|EB160286
EST:     CTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: CTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
EST: gi|78077113|gb|DV505547.1|DV505547
EST:     GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT                         CTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC
genomic: GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTC

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: 45 (upstream exon), 34 (downstream exon)
Score: 64

GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC


Block sizes: 45 (upstream exon), 37 (downstream exon)
Score: 131

GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 238

GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC


Block sizes: 45 (upstream exon), 34 (downstream exon)
Score: 167

GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattat ... ccccttccagCTCCATATCTTATTCTGTGTCTGGTCAGCTGTGGCTCCTCCATTTCCATTCAAAGGAAAATCCTTGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTTgtaagattatcatcacttcatatattagaaaaaatatatttcactccctgctaatgatctttaccccttccag

- - - - - -  TTGAAG