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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatctcttcaaattaatctttcgctttattgtttcgttatgctttagcctttgtcatatcttagttttctgcttggtgttgaccatcattctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG

Basic information

species Zea mays
transcript GRMZM2G088397_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g45390.2 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------gtccatctcttcaaattaatctttcgctttat----tgtttc--gttatgctttagcctttgtcatatcttagttttctgcttggtgttgac-----catcattctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
                                                             || |||||  | || | | |    |    ||     ||||||  | |    ||     || |||||   ||| ||   || ||| || ||||      ||  | | | || ||| || |||||||||||||| |||||||||||||| ||||
gtccgtgtttttcttattcaaatttccatagcattaaaaaatgccctttcgtctgttctttgttcatctagttaattgattacaacaaaataccagatgtttcaggcttcctttctaaattagtcattagttatttacttgtttg-tgatgacatatttattttacctaaaacagATGCATCAAAATTGCTATCGTGCATGACATTGCTGAAG
















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|26557485|gb|CA829720.1|CA829720
EST:     GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAG                         GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
genomic: GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
EST: gi|211066808|gb|FL430471.1|FL430471
EST:     GCCTTGATGGCTCTGATTGSKGGTGATCTGCCTGCTGTGGATCGAGAAAG                         GTGTATCAAAATTGCTATTGTGCATGACA
genomic: GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACA
EST: gi|211108462|gb|FL406879.1|FL406879
EST:     GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAG                         GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGCTATTG
genomic: GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAGCTATTG
EST: gi|32840843|gb|CD980524.1|CD980524
EST:     GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAG                         GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
genomic: GCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
EST: gi|194717181|gb|FK934334.1|FK934334
EST:     CCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAAG                         GTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
genomic: CCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAG-AAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG

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: 42 (upstream exon), 48 (downstream exon)
Score: 56

ACCATAGCATCAAGGGCCCTGAGTCCATTGCTGATCACATGTACCGAATGGCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 46

ACCATAGCATCAAGGGCCCTGAGTCCATTGCTGATCACATGTACCGAATGGCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 39

ACCATAGCATCAAGGGCCCTGAGTCCATTGCTGATCACATGTACCGAATGGCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 45

ACCATAGCATCAAGGGCCCTGAGTCCATTGCTGATCACATGTACCGAATGGCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctct ... ctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcctttgtcatatcttagttttctgcttggtgttgaccatcattctttaatcagGTGTATCAAAATTGCTATTGTGCATGACATTGCAGAAG
                               tgttgac  putative branch site (score: 45)
                                        tcattcttt  putative PPT
                                          attctttaat  TA-rich tract