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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgtttatgactctacgcactgcaatgggtggaaatttttctctttctgcaacaatttagtggatgacatgttttttgtcactactccctccaggt...

Basic information

species Zea mays
transcript GRMZM2G038313_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038313_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G16090.1 (Glycine max), 5'ss of exon 6
GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgtttatgactctacgcactgcaatgggtggaaatttttctctttctgcaacaatt-tagtggatgacatgttttttgtcactactccctccaggt----
| || |||   ||||| ||  | || | ||||||||||||||||||  | || ||||| ||||||||||||||  | || || |   ||||||| ||  |||  |    |   | |  |   | ||   | | |   ||  | ||| |  ||  |    || |  |     |||  |||                | | ||    
GCAACTTTTCAACTGTACCGCTAAGGGATGAGTTCCTTGAAAATGCTAGGCTATTTATCTTCGAGACATACTGTAGAATACACCAACGCATTGACATGGGgtatgcaccttctaat--ataaaatgttgtagct---aagctctctttgcctatagtttttctgatatgctacaattttgcacctgtggaaaatgcaatgtagcc

upper sequence: GRMZM2G038313_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 6
GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgtttatgactctacgcactgcaatgggtggaaatttttctctttctgcaa-caatttagtggatgacatgttttttgtcactactccctccaggt----
|||  |||   ||||| || ||||| | |||||| || ||||||||||| || |||||||| |||||||||||||| || ||||   | ||||| ||  |||   | ||||| ||| |  | | |   ||   |  |  ||  |   |||    |  ||| ||  | ||  |||  ||  ||  ||   || | |   ||     
GAAGCTTTTCTACTGTGCCATTGAGGGATGAGTTTCTCGAAAATGCCCGGCTTTTTATTTTTGAGACATACTGCCGAATACATCAACGAATTGACATGGGgta--tatttat-actttctgaaatttgattaatatagcttcattctttttgataggcaaattgatagactaca--ttgattagcatagcttcatgtgggagtgc
















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|33097754|gb|CF057714.1|CF057714
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|32928420|gb|CF033232.1|CF033232
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|32928859|gb|CF033671.1|CF033671
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|71333150|gb|DR803609.1|DR803609
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|211376028|gb|FL471754.1|FL471754
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|71759147|gb|DR957084.1|DR957084
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGTTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|148943092|gb|EC888146.2|EC888146
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|211376029|gb|FL471755.1|FL471755
EST:     TGTTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: TG-TTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|32929145|gb|CF033957.1|CF033957
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|76919395|gb|DV167694.1|DV167694
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|71318806|gb|DR796164.1|DR796164
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|88754908|gb|DY539049.1|DY539049
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|32803563|gb|CD955799.1|CD955799
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTAAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
EST: gi|86467967|gb|DY234337.1|DY234337
EST:     CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAG                         CATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT
genomic: CTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGAT

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: 232

GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGATAATGAACTTGGTTAGGAGCTCAAAACTGGATGCAAGGATCGATTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGATAATGAACTTGGTTAGGAGCTCAAAACTGGATGCAAGGATCGATTCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGATAATGAACTTGGTTAGGAGCTCAAAACTGGATGCAAGGATCGATTCAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgttt ... caatgtacagCATGCTTGCTCAGAGGCTGAACATGAGCTACGATGAGGCCGAGTTGTGGATAATGAACTTGGTTAGGAGCTCAAAACTGGATGCAAGGATCGATTCAGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATTTTGTCACTGTTCCTTTGAGAGCTGAGTTCCTTGAAAATGCCCGACTGTTTATTTTCGAGACATACTGCCGTATCCATCGGTGCATTGATATCAGgtgggtgtttatgactctacgcactgcaatgggtggaaatttttctctttctgcaacaatttagtggatgacatgttttttgtcactactccctccaggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctcc