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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctctgtctctttgcccccatttcaatatcctcatggctccatctccaggtcgtcaaacagtacctgagacatgacctgggctgggattgaatcatgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA

Basic information

species Zea mays
transcript GRMZM2G437859_T04
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g55500.1 (Oryza sativa), 3'ss of exon 13
gttcgtctctgtctctttgcccccatttcaatatcctcatggctccatctccag-gtcgtcaaacagtacctgagacatgacctgggctgggattgaatcatgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA
    |  | | |||  || |    ||   | |  |      | | | |||  || || || |   | |||   ||  |  | ||    || |  || || |||     ||||||||||||||||||||||| |||||||| ||||| ||||| || || ||||| |||||||| ||||||||||||||||||||||||||  | || | ||
--aagattatttctacttacaataatactagttgcagtggagattcttctgaagcgtagttaggaattac---aggtactaacttttgtgtg-ctgtataatg-----cagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTGATCGTGGCCGTCTTCCTGGACAACACGCTGGAGGTGAAAAACGCGGCCA
















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|91049744|gb|EB160162.1|EB160162
EST:     GTTACACCATGGCTGTTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTTTCTTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|149071735|gb|EE160128.2|EE160128
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCANNNNNNNGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|71759661|gb|DR957598.1|DR957598
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|50337438|gb|CO532564.1|CO532564
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|50337437|gb|CO532563.1|CO532563
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTCTTGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|76287139|gb|DV026707.1|DV026707
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|76287138|gb|DV026706.1|DV026706
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG
EST: gi|71310985|gb|DR791794.1|DR791794
EST:     GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGG                         TTCAACGACTACATCAACACCATCTTTTCGTCGCCGCCGACCGTGGGGCTG
genomic: GCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTG

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: 155

CGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGAATACTTTTTCCGCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 40

CGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGAATACTTTTTCCGCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 14

CGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGAATACTTTTTCCGCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 9

CGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGAATACTTTTTCCGCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctct ... tgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcaaacagtacctgagacatgacctgggctgggattgaatcatgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA
                                    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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtctctgtctctttgcccccatttcaatatcctcatggctccatctccaggtcgtcaaacagtacctgagacatgacctgggctgggattgaatcatgaatggcagTTCAACGACTACATCAACACCATCTTCTCGTCGCCGCCGACCGTGGGGCTGATGGTGGCCGTGTTCCTGGACAACACGCTGGAGGTGAAGCAAGCCGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGCCGCCG