Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaacaattatttatgaatccaatgtgtttgttaacagggttacaaaaacacagcacatgcgctgtttgataactagtgattattatgtctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG

Basic information

species Zea mays
transcript GRMZM2G007915_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007915_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------------------------tttaacaattatttatgaatccaatgtgtttgttaacagggttacaaaaacacagcacatgcgctgtttgataactagtgattat-tatgtctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG
                                                                                      |||||||  |  | |||| | | ||  ||| || ||  ||||| ||| ||  | ||   |  ||||||||     | |  || | | || |||| |||||||| ||||| || || |||||||||||||| ||||  || ||||  ||||| ||||| |||||||||||||| |||||||||||| |||| || |  || 
gtgagttcactacttttctgagtcttattttaaattttggtttcgacttggaatatttatttatccccaagattgtttaactataattaacaagcacatctgaagcgattg-atttcttgaccaggttagaaacacttaacatg-gttctgtttgaagtgcattatttttctttgactatctgcagGTATAACGGCCTTGATGGAACACACATTAATGTAAGCGAATTTGCAAGAGAGAAAGACTGCCTTGTATGTGGACCTGGTACCCTTATTGAACTTGGGACA
















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|67018949|gb|CO447698.1|CO447698
EST:     GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|78124195|gb|DV542579.1|DV542579
EST:     GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|71419961|gb|DR804957.1|DR804957
EST:     GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|60398591|gb|DN231407.1|DN231407
EST:     TGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: TGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|71760307|gb|DR958244.1|DR958244
EST:     AAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: AAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|5847480|gb|AW000559.1|AW000559
EST:     GTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACGCACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|71311092|gb|DR791860.1|DR791860
EST:     GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|149099068|gb|EE185088.2|EE185088
EST:     GCCTTAAAGCTTATTTCTGGGGGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|76287586|gb|DV027154.1|DV027154
EST:     GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|5901235|gb|AW042335.1|AW042335
EST:     GTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACGCACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
EST: gi|211475001|gb|FK984421.1|FK984421
EST:     GCCTTAAAGCTTATTTCTGGGTGCARCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGT
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGT
EST: gi|71431173|gb|DR812223.1|DR812223
EST:     GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCAC                         GTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA
genomic: GCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGA

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: 402

CAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 247

CAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 344

CAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 272

CAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCAAAAGTGTGTCAAACTATCTCACgtgagttcca ... ctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaacacagcacatgcgctgtttgataactagtgattattatgtctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG
                       tgataac  putative branch site (score: 272)
                                            tctattt  putative PPT
                                   attattatgtctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaacaattatttatgaatccaatgtgtttgttaacagggttacaaaaacacagcacatgcgctgtttgataactagtgattattatgtctatttgcagGTACAACGGTCTGGAAGGAACACACATTAAAGTAACTGAGTTTGTCAGAGACAAAGATTGCCTTGTATGTGGGCCTGGTACCCTTGTTGAGCTGGATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - -tgaatcc
- - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcgc