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

gtgctgtgctctcctcggatttgctttgttctatcattatgtttcgccagggccatagttttcttaagaacgatgaagatgctcactgctagtatatgtctggcggttttatactcatgcatttttgccttctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT

Basic information

species Zea mays
transcript GRMZM2G052630_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 4
gtgctgtgctctcctcggatttgctttgttctatcattatgtttcgccagggccatagttttcttaagaacgatgaagatgctcactgctagtatatgtctggcggt--tttatactcatgcatttttgccttctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
                |   || |     || ||||   |||   ||    | || | |    |    ||| ||  |     | | || |   |  || |||    |   |  |  | |||  ||||  |||| ||| | ||||| ||||||||||||||| | |||||| |||| ||||| ||||||||||
----------------gtgcttccccaaatc-atcaacttgtactgcttcagtcagactccagtgttaaacaatttactcatttagtgttctca-gtgactgataatggatcctgttaatgtgtttt-accttttctctaaagctaatcagTGGGGAGCATGTGGGGGCATTGGCGATGAGCGAACCCAACT

upper sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 5
gtgctgtgctctcctcggatttgctttgttctatcattatgtttcgccagggccatagttttcttaagaacgatgaagatgctcactg-ctagtatatgtctggcggtt--ttatactcatg---catttttgccttctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
                                              | ||   |||   | |  ||      | ||  ||  |   |   ||   | | ||||   |||  || |||| |||    || | || | | | | | ||||||||||||||||||||| | || || || |||||||||||||||||  
----------------------------------------------ctagaatcatccatctgatattggtcaagattatttttcttaattatcctttatctgagtgttctttgtactaatgaagtatatctgtcatgttt-taaagCTCATCAGTGGGGAGCATGTAGGAGCTCTTGCAATGAGTGAACCCAATG
















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|67030645|gb|CO459394.1|CO459394
EST:     GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTG--C---                         C-CA--AGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
EST: gi|31354622|gb|CD438979.1|CD438979
EST:     GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG                         CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
EST: gi|76936508|gb|DV174756.1|DV174756
EST:     GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG                         CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     AGCTTGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG                         CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: AGCTTGTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
EST: gi|149079538|gb|EE168523.2|EE168523
EST:     GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG                         CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
EST: gi|91057188|gb|EB167606.1|EB167606
EST:     GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG                         CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
EST: gi|149073457|gb|EE161762.2|EE161762
EST:     GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAG                         CTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
genomic: GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT

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: 48 (upstream exon), 44 (downstream exon)
Score: 35

GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT


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

GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 39

GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 27

GTCCGGCACGGCAGTCCCGAGCAGAGGCTCAAGTATCTGCCCAAGgtgctgtgct ... ctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctagtatatgtctggcggttttatactcatgcatttttgccttctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT
                                 catttttgccttctct  CT-rich tract
                    ttttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgtgctctcctcggatttgctttgttctatcattatgtttcgccagggccatagttttcttaagaacgatgaagatgctcactgctagtatatgtctggcggttttatactcatgcatttttgccttctctatgaagCTCATCAGTGGGGAGCATATCGGGGCACTGGCAATGAGTGAACCCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA