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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttctatgtgtagtttcgtcatgatgcttctgtcaactctgctgatactgtatcttgtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG

Basic information

species Zea mays
transcript GRMZM5G823484_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g13590.2 (Oryza sativa), 3'ss of exon 19
gtaagtgttctatgtgtagtttcgtcat---gatgcttctgtcaactctgc-tgata----ctgtatcttgtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG
|| ||||  |  ||| |  | |  |      |||| |||| | |    | | | |||     | |||    |||||||||  |||| || || ||||| |||||||| |||||| |||| ||| | ||||||||||||||||| ||||| || ||||||||| |
gtgagtgcgccttgtatcttgttatttctcagatggttctctaagtcgtccctaatataatttctattgcttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGAAGGAACCCCCAGTATCCGGAAAGATGCCTTGCG
















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|93283185|gb|EB675449.1|EB675449
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|67013225|gb|CO441974.1|CO441974
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|60356127|gb|DN223100.1|DN223100
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|78027269|gb|DV495656.1|DV495656
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|4834925|gb|AI670151.1|AI670151
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|91878412|gb|EB408369.1|EB408369
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|9731461|gb|BE510213.1|BE510213
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|37392304|gb|CF633401.1|CF633401
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|9461397|gb|BE453712.1|BE453712
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|76012574|gb|DT939744.1|DT939744
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|6672239|gb|AW282405.1|AW282405
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|37377535|gb|CF625382.1|CF625382
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|60396240|gb|DN229109.1|DN229109
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
EST: gi|5847426|gb|AW000505.1|AW000505
EST:     CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAAT                         TGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA
genomic: CGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGA

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), 49 (downstream exon)
Score: 71

TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 73

TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 53

TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 71

TGGTGGCCTACGGTTGAAACGTGACATAACTGAATATGGGGATTTCGTTCGTAGCTTCAATGCCCCCTCCATAGATGAGAAGTTCGAACTGTTGGGAATgtaagtgttc ... gtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcgtcatgatgcttctgtcaactctgctgatactgtatcttgtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG
                            tgctgat  putative branch site (score: 71)
                                           ttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttctatgtgtagtttcgtcatgatgcttctgtcaactctgctgatactgtatcttgtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG