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

gtaagaacaaagaaccattctttaagctaacttggtttgttgttacttgcttaatattgtatctagctatctacagttttgcaacactaacaatttttatgggatagaatttctctaatactagagaatgaaatttcagtatcttctagcaatgtagcataaatatctgacttactcctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT

Basic information

species Zea mays
transcript GRMZM5G886952_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G886952_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g16010.1 (Oryza sativa), 3'ss of exon 3
gtaagaacaaagaaccattctttaagctaacttggtttgttgttacttgcttaatattgta-tctagctat--ctacagttttgcaacactaacaatttttatgggatagaatttctctaatacta-gagaatgaaatttcagtatcttctagcaatgtagcataaatatctgacttac----tcctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT
|||||| ||||     |  |  ||    ||       | |||| |  ||||||  |||  |  || |||||   |    ||  | || |         ||| |  ||| | |||| |||||||  | | |||||| |  |   || ||||   || |||   | | |||||||||   |    || ||| || |||||||||||||| ||||  ||||||||||||||||| || |||||||||| |||||||||||||||| |  |
gtaagaccaaaa---taaaccctacataaa-------tattgtgaaatgcttagaatttcaacctggctattattttgcttcagtaatatggttttcgtttttaagatggcattt-tctaataggaagggaatgataacttcatagcttc---cattgttataaatatatctgaccaccaatatcttttgtttagGATTCTTGCATATCACAAGTTAGTTGGGCCCATACCTCCAGAAATTGGAAGGTTAAATCAGTTGCAAGCTCT
















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|60356786|gb|DN223759.1|DN223759
EST:     AGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|211489917|gb|FL021476.1|FL021476
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGTAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|211487045|gb|FL021472.1|FL021472
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGTAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|149109166|gb|EE190051.2|EE190051
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|148951631|gb|EC897373.2|EC897373
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|31360094|gb|CD444451.1|CD444451
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|149087972|gb|EE177200.2|EE177200
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|149087580|gb|EE176978.2|EE176978
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|31354140|gb|CD438497.1|CD438497
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
EST: gi|31349376|gb|CD433733.1|CD433733
EST:     AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCT                         GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA
genomic: AATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAA

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: 213

ATTCAGATGGAGTCTTTCTAAATTGGCGTGAGCAAGATGCAGACCCCTGCAATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

ATTCAGATGGAGTCTTTCTAAATTGGCGTGAGCAAGATGCAGACCCCTGCAATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 34

ATTCAGATGGAGTCTTTCTAAATTGGCGTGAGCAAGATGCAGACCCCTGCAATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 147

ATTCAGATGGAGTCTTTCTAAATTGGCGTGAGCAAGATGCAGACCCCTGCAATTGGAAGGGTGTTAGATGTGATAGTCATAGCAAGAGAGTGATTGATCTgtaagaacaa ... ctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcagtatcttctagcaatgtagcataaatatctgacttactcctttattcagGATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCCGAAATTGGAAAGTTAAATCAGTTGCAAACCTT
                                    gacttac  putative branch site (score: 147)
                                      cttactcctttattc  CT-rich tract
                          ataaatatct  TA-rich tract