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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttattttatttgttttttaatgaaaaaaatagttaacctttcatatctatacttgtgcttgaatacatatgtccctgctgactcgttctactgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT

Basic information

species Zea mays
transcript GRMZM2G103473_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103473_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 3'ss of exon 6
gtggttat--tttatttgttttttaatgaaaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatatgtccctgctgactcgttctact-gcactcagTGATAA-CAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||   ||   | |||| || || |  | |||  || | |||||| |   ||  |||| | ||| |  |        | ||||||     | || |    ||| || || |||||||||||||||||||||| |||||||||| |  |  ||||| || ||||| ||| | |||||||||||||||||| | ||||||||||| 
gtgattatgccttcacttttttctagtgcagtagata--tagcatttcattttactatgttgtacctgatt-tagccaattatcctgacttagcgtgcttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCATCAGATTTTGTGGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACAT-

upper sequence: GRMZM2G103473_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
gtggttattttatt-tgttttttaatgaaaaaaatagttaacctttcatatctatacttgtgcttgaatacatatgtccctgctgactcgttctac-tgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||| | |  |  ||| || |  |  | |||    |  | |  |  | ||  |||| |   |  | |        | ||||||   | | | ||    |||||| |||||||||||||||||||||||| | |||||||| |  |  ||| | || ||||| ||||| |||||||||||||||||| | |||||||| |||
gtgattattctttcattgtttctagtccagtagatatagcatttctttttaccatg-ttgtaccc-atcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
















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|166687848|gb|EG095729.1|EG095729
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGAC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGAC
EST: gi|5688730|gb|AI941745.1|AI941745
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATC
EST: gi|149101188|gb|EE187299.2|EE187299
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATC
EST: gi|45567981|gb|CK985842.1|CK985842
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATC
EST: gi|71761777|gb|DR959714.1|DR959714
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATC

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: 28 (upstream exon), 49 (downstream exon)
Score: 35

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT


Block sizes: 21 (upstream exon), 49 (downstream exon)
Score: 24

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 19

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT


Block sizes: 11 (upstream exon), 45 (downstream exon)
Score: 4

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatacttgtgcttgaatacatatgtccctgctgactcgttctactgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT
                              tgctgac  putative branch site (score: 4)
                                        ttctact  putative PPT
                aatacatat  TA-rich tract