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'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattttcccctttccttttctactgaaattattaaatgttatatgctgatatgcctcgttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT

Basic information

species Zea mays
transcript GRMZM2G047695_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 8
gtgagaatt----ttcccctttccttttctactgaaattat-----taaatgttatatgctgatatgcctc-gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT
||| ||| |    || || ||| |||||| | |   | |        ||||||| |||  ||| ||||||  | || || |||||| ||| |||||||||||  ||||  |||||||||||||||| |||||||| ||||| ||||| ||| |||| ||||||||||| || ||||| ||||
gtgggaactatgatttcctttttcttttccatttggaatgcaactacaaatgttgtatattgacatgccttaggtgcattagGTCTGTGTGGGTAAAGAGAAGGAAACAATTGCAGAAATGCTGCCCTATTTGAGGCTAGGATACATTTCAGATCCAGATGAAATGCAATCCATACTTTCTT
















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|31350131|gb|CD434488.1|CD434488
EST:     AGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAAT                         GTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTG
genomic: AGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTG
EST: gi|71449280|gb|DR830330.1|DR830330
EST:     AGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAAT                         GTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTG
genomic: AGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTG
EST: gi|15209056|gb|BI430940.1|BI430940
EST:     AGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAAT                         GTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTG
genomic: AGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTG

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), 47 (downstream exon)
Score: 49

GCATCTTTAAATACAGAAGATCCTCAATACCAAGAAAAGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GCATCTTTAAATACAGAAGATCCTCAATACCAAGAAAAGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 49

GCATCTTTAAATACAGAAGATCCTCAATACCAAGAAAAGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 129

GCATCTTTAAATACAGAAGATCCTCAATACCAAGAAAAGAGAATGGTTGCTCAGAGGAATGGAAAACTTGCTATCCAAAATTTTAATgtgagaattt ... gttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttctactgaaattattaaatgttatatgctgatatgcctcgttgaatcagGTCTATGTAGGTAAAGAGAAACAAACTGTTGCAGAAATGCTGCCTTATTTGAGACTAGGTTACATATCAAATCCTGATGAAATGCAGTCTATACTCTCTT
                               tgctgat  putative branch site (score: 129)
                                         cctcgtt  putative PPT
     ttctactgaaattatt  TA-rich tract