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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttacttcattattgttcgttagtcaagattagtttatcacaagtcttagtgttttatcttgaccagtttaatgttaatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG

Basic information

species Zea mays
transcript GRMZM2G006428_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 12
gtatttacttcattattgttcgttagtcaagattagtt-tatcacaagtcttagtgttttatcttga-ccagtttaatg---ttaatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG
            ||| | ||| || | |||| |||||| | ||| ||| ||    | | | || ||  | ||||||||    | |||   |||||||||||||| || ||||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||
-----------gttagttttcatt-gccaagtttagttctctcataagcctcctagatctctcatgggcgagtttaataatttcaatacgcagATTGTCGAATGTAGGAGGGTATTGAAGTGGACTTATGCTTATGGTTTTTACCTCCCAGAGCATGAACATGCCAAAAGACAGTTCTTTGAATATCTGCAAG

upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 12
gtatttacttcattattgttcgttagtcaagattagtttatcacaagtcttagtgttttatcttgaccagtttaatgttaatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG
        | |||  | | |  |  | ||       | | | | | ||  |  |||||  |||| ||   |    |||     | ||||| || ||||| ||  | ||  | || ||||| ||||||||||||| |||  | || |||||||| ||||| || |||||||||||||| ||  ||||||
-------gtacatagtggattct--gccattgcacatct-tgaaaggtactgctgtttcttctt-actgttgccttgtc----tgcagATAGTTGAATGTAGGCGAGTTCTAAAATGGACATATGCCTATGGATATTATTTACCTGAGCATGAACATGCTAAGAGACAGTTCTTTGAGTACTTGCAAG

upper sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------------------------------------------------------------------------------gtatttacttcattattgttcgttagtcaagattagtttatcacaagtcttag-tgttttatcttgaccagtttaatgttaatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG
                                                                                                         ||| | ||      | ||  |  |  |||  |  ||   |||||     |  ||| ||   || |   ||||  | ||  ||| |||||||| |||||| |  | |||||||||||||| ||||| ||||||| |||| | || ||| |||||||  | |||||||| |||||||||||   |||||
gttaatacactttgtgcgtggacatgttatttttgcgcttgctggatatcctttgtcttaattacgttatttattgcatataatgcggagtatggagtgtggaacattcatttggagcatttttctcgg--aagcatcattatccacaatcacaaactgtattccttttaatcgttt--ttttgttgtgcagATTGTAGAATGCCGGCGTGTATTGAAGTGGACATATGCTTATGGATATTACTTACCTGAGAATGAGCACACGAAAAGACAATTCTTTGAATACTCGCAAG

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|211292139|gb|FL375498.1|FL375498
EST:     AAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG                         ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTAC
genomic: AAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTAC
EST: gi|78080365|gb|DV508777.1|DV508777
EST:     AAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG                         ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTAC
genomic: AAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTAC
EST: gi|26559234|gb|CA831469.1|CA831469
EST:     AAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAG                         ATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTAC
genomic: AAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 128

CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 88

CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 110

CTTGAAAGGTTAAGTGACATACAAAGTCAACCTGAGTCACAGCTGAAGTTCATTATAGAGGCATGGTTACAGgtatttactt ... taatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttatcacaagtcttagtgttttatcttgaccagtttaatgttaatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG
                                          tgttaat  putative branch site (score: 110)
                                     tttaatgttaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttacttcattattgttcgttagtcaagattagtttatcacaagtcttagtgttttatcttgaccagtttaatgttaatgtacagATTGTCGAATGCAGAAGGGTATTGAAGTGGACTTATGCCTATGGATTTTACCTGCCAGAGCATGAGCATGCCAAAAGACAGTTCTTTGAATATCTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA