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

gttgccagctgaaacattttaaattttgctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA

Basic information

species Zea mays
transcript GRMZM2G010494_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g19740.1 (Oryza sativa), 3'ss of exon 2
-gttgccagctgaaaca--ttttaaattttgctttgccttcttctgatactt--------aaattg---atatctaaacttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA
  |||||   || |  |  ||||||| ||||||||  |  |||||| |  |         |||||    || ||||||   ||||||||  ||| ||||||||| |||||||||||||||||||||||||| ||||| ||||||||||||||||||||| | |||||||| ||| ||||  ||||| ||||||| ||
gtttgcctcttgtactaatttttaaagtttgctttatccccttctggtgttcttccggaaaaattacctatctctaaaaccttctgatgttatgcagGTCCTCTGGGGCAGGGTTTTGCAAATGCTGTTGGCCTAGCGCTTGCTGAGAAACATCTAGCTGCCCGTTTCAATAAGCCTGATTTGAAAATCGTGGATCA

upper sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
gttgccagctgaaacattttaaattttgctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgt--agGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA
|||    | |  |    ||||  ||    ||  | |  |     |  ||    || | | |    | | || | |   |||  |||||||||||| |||||  |||| |||||||||||| ||||||| |||||||| ||  | ||| |||| || |||||| ||||||   |  | || |||||
gttagatgtttcattggtttatgttactgttatcatggtgagcctttttgctgtgttctgttgcttatcctcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
gttgccagctgaaacattttaaattttgctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgt--agGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA
|||      |  |  | ||||  || |  ||  | |  |     |  ||    ||   | |    | | ||  ||   |||  |||||||||||| |||||  |||| |||||||||||  ||||||| |||||||||||  | ||| |||| || |||||| ||||||   |  | || |||||
gttagatatttcattagtttatgttattgttatcatagtgagcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgccagctgaaacattttaaattttgctttgccttctt-ctgatacttaaatt----gatat----ctaaacttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA
   |  || |  |   | |    || |  | ||  || |   ||||  | |  ||     ||||     |     | | ||    |||| |||||||||||| || ||| ||||||||||||||||  |||| ||||| ||||| ||| | ||| |  | || |||||  ||||||   |  | || |||||
---gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

upper sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
-------------gttgccagctgaaacattttaaattttgctttgcctt-cttctgatacttaaattgatatctaa--acttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA
              |||   | | || |  |||    ||||||   || | |  | ||  | |   |    ||||    || |   |       ||||||||||||||| |||||| |||| |||||||||||  | || ||||| ||||  ||  | ||| | || ||||||||  | ||||   |  | || || ||
gttagattctagtcttgaatgttaaatctgttttg--tttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA

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 3 RNA-Seq libraries.


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 21

ATGGACGATCTGAAAACTTTCCGACAATGGAGAAGCAGAACTCCTGGTCACCCAGAAAATTTTGAAACACCTGGCGTTGAAGTCACCACAGgttgccagct ... tgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA


Block sizes: 16 (upstream exon), 34 (downstream exon)
Score: 1

ATGGACGATCTGAAAACTTTCCGACAATGGAGAAGCAGAACTCCTGGTCACCCAGAAAATTTTGAAACACCTGGCGTTGAAGTCACCACAGgttgccagct ... tgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA


Block sizes: 47 (upstream exon), 17 (downstream exon)
Score: 3

ATGGACGATCTGAAAACTTTCCGACAATGGAGAAGCAGAACTCCTGGTCACCCAGAAAATTTTGAAACACCTGGCGTTGAAGTCACCACAGgttgccagct ... tgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgccttcttctgatacttaaattgatatctaaacttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA
                                       ttctgat  putative branch site (score: 3)
                   ttaaattgatatctaa  TA-rich tract