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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaggtcaaaacagccatccttgagagtgaacctgagatgcgctcaacagctaacatattccgtcttcgttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA

Basic information

species Zea mays
transcript GRMZM2G109987_T05
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109987_T05 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 3'ss of exon 18
---------------------------------------gttagaggtcaaaacagccatccttgagagtgaacctgagatgcgctcaacagctaacatattccgtcttcgttgt---tttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA
                                        | | |  ||| ||    |    |||| | | ||    |  |  | |  |  ||| ||   ||   ||   ||| |   |||||||| | |  |||||||| |||||||||||||||||||||||||| || |||||||||||||| || || || || ||||| ||||| | |||||||||||
gtagaaactccttttcgcttaactcacacccttaagtgcatcatatttcagaaatcgctgagttgaaa-taaattaaaattatgttacattgcttaccatttttttccctgttttgtgtttagGGCCATGTCTACCTGCCATCAGGCGTGTGCATGTCAGGAATGGGTCGGCATGTTTCTTTCGATCAGGCCGTGGCTTGGAAAGTGCTTGCCGAGGATAGCA
















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|5688528|gb|AI941543.1|AI941543
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|166621677|gb|EG177308.1|EG177308
EST:     ATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: ATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|14244886|gb|BG842824.2|BG842824
EST:     AGTCAGGAAGGAAAGCACTATTTTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|30032082|gb|CB833933.1|CB833933
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGAACACCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|211351868|gb|FK984283.1|FK984283
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCASS--TGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|101391393|gb|EB817631.1|EB817631
EST:     AGTCAGGAAGGAAAGCACTATTTTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|211351870|gb|FK984285.1|FK984285
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|31350140|gb|CD434497.1|CD434497
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|4681163|gb|AI629833.1|AI629833
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
EST: gi|32835598|gb|CD975276.1|CD975276
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCT
EST: gi|211247735|gb|FL065573.1|FL065573
EST:     AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAG                         GGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT
genomic: AGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCAT

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), 48 (downstream exon)
Score: 185

AACATCTCTTGTTGCCCTGCAAGACCTGACGCTAGACAAGATCTTCGACGAGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 55

AACATCTCTTGTTGCCCTGCAAGACCTGACGCTAGACAAGATCTTCGACGAGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 64

AACATCTCTTGTTGCCCTGCAAGACCTGACGCTAGACAAGATCTTCGACGAGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 52

AACATCTCTTGTTGCCCTGCAAGACCTGACGCTAGACAAGATCTTCGACGAGTCAGGAAGGAAAGCACTATTCTCAGACATCTCGAAACTAATGGAACAGgttagaggtc ... gttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtgaacctgagatgcgctcaacagctaacatattccgtcttcgttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA
                         agctaac  putative branch site (score: 52)
                                        tcttcgtt  putative PPT
                            taacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaggtcaaaacagccatccttgagagtgaacctgagatgcgctcaacagctaacatattccgtcttcgttgttttagGGCTACGCGTACCTGCCGTCAGGCGTGTGCATGTCAGGAATGGGCCGCCATGTTTCTTTCGACCAAGCTGTAGCGTGGAAGGTGCTCGGCGAGGATAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT