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

gtatgtttcagattcttatgtgttactctgtatcgttttttctttacctattttttactatctgattgaatgtaactaacaccgtagtcatgtcatccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG

Basic information

species Zea mays
transcript GRMZM5G825902_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109785_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 5
---------gtatgtttcagattctta--tgtgtt---actctgtatcgttttttcttt---acctattttttactatctgattgaatgt----aactaacaccgtagtcatgtc-atccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG
         |   ||  ||   | |||  ||||||   |   | || ||||  |  |||   | |  || ||   | | ||| | || ||    ||||||| |  | |||  ||  ||     ||||||||||||||||||| ||||||||||||||||||||||| |||||| ||||||||||||||
gtatgttccgagcgtcacatccttttacttgtgtttagaacttctaccgttagtaattttggatccgttcttgtttttatgaatcaaagtatcaaactaactcatttgtctggttgatatgcatgtagGAATCAAGTGAGAATTTAGCCATGGGTGAATTTTTTGGAATAAAAGCTCCTGAGAAGAAG
















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|31351917|gb|CD436274.1|CD436274
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAAATCA-GTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCC
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAA-TCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCC
EST: gi|213192723|gb|FM191866.1|FM191866
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|26558566|gb|CA830801.1|CA830801
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAG
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAG
EST: gi|67035504|gb|CO464037.1|CO464037
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|31355619|gb|CD439976.1|CD439976
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|31356321|gb|CD440678.1|CD440678
EST:     TAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|31353042|gb|CD437399.1|CD437399
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|211133671|gb|FL369481.1|FL369481
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|60394317|gb|DN227187.1|DN227187
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|31360452|gb|CD444809.1|CD444809
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|149100918|gb|EE187014.2|EE187014
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|87157787|gb|DY402576.1|DY402576
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGG
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGG
EST: gi|8516597|gb|BE123322.1|BE123322
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|5847192|gb|AW000271.1|AW000271
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|5325091|gb|AI783282.1|AI783282
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|22545865|gb|BU098239.1|BU098239
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|149074678|gb|EE163096.2|EE163096
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|71447368|gb|DR828418.1|DR828418
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|6526657|gb|AW215948.1|AW215948
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAA
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAA
EST: gi|148999647|gb|EE036634.2|EE036634
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|6194493|gb|AW146597.1|AW146597
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|31363719|gb|CD448076.1|CD448076
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|5871295|gb|AW017766.1|AW017766
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTTTCCAGTACCATCCT                         GAATCAAGNGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|5860476|gb|AW011698.1|AW011698
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
EST: gi|5871459|gb|AW017930.1|AW017930
EST:     TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT                         GAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT
genomic: TAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCT

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: 350

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 545

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 768

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 561

TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCTgtatgtttca ... ccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttactatctgattgaatgtaactaacaccgtagtcatgtcatccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG
                      aactaac  putative branch site (score: 561)
                                         tcatcctt  putative PPT
             attgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcagattcttatgtgttactctgtatcgttttttctttacctattttttactatctgattgaatgtaactaacaccgtagtcatgtcatccttgtgtagGAATCAAGTGAGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG