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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttattttctttgttttttaatgacaaaaatagttaacctttcatatctatacttgtgcttgaatacatacgtccctgctgacgcgttctactgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT

Basic information

species Zea mays
transcript GRMZM2G164175_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 3'ss of exon 6
gtggttat--tttctttgttttttaatgacaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatacgtccctgctgacgcgttctact-gcactcagTGATAG-CAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||   |||  | |||| || ||    | |||  || | |||||| |   ||  |||| | ||| |  |  |     | |||||      | || |    ||| || |  ||||||||||||||||||||||||||||||||| |  |  ||||| || ||||| ||| |||||||||||||||||||| | ||||||||||| 
gtgattatgccttcacttttttctagtgcagtagata--tagcatttcattttactatgttgtacctgatt-tagccaattatcctgacttagcgtgcttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCATCAGATTTTGTGGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACAT-

upper sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
gtggttattttctttgttttttaatgacaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatacgtccctgctgacgcgttctac-tgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||| | ||  || |||   | | |  | |  || | |||| | |    |  |||| |   |  | |  |     | |||||    | | | ||    |||||| | |||||||||||||||||||||||| |||||||| |  |  ||| | || ||||| |||||||||||||||||||||||| | |||||||| |||
gtgattattct-ttcattgtttctagtccagtagatatagcatttctttttaccatgttgtaccc-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|71427411|gb|DR808461.1|DR808461
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71314140|gb|DR793687.1|DR793687
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|40336287|gb|CK370357.1|CK370357
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71764471|gb|DR962408.1|DR962408
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|6654204|gb|AW267609.1|AW267609
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|88748600|gb|DY532741.1|DY532741
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71321848|gb|DR797614.1|DR797614
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|76932561|gb|DV173073.1|DV173073
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|4826073|gb|AI667701.1|AI667701
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211236953|gb|FK974486.1|FK974486
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTKGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211236952|gb|FK974485.1|FK974485
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|148948729|gb|EC898651.2|EC898651
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATT
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|37392942|gb|CF633725.1|CF633725
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211131602|gb|FL458961.1|FL458961
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTYCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC

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: 80

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 60

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 74

GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatacttgtgcttgaatacatacgtccctgctgacgcgttctactgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT
                              tgctgac  putative branch site (score: 74)
                                        ttctact  putative PPT
                aatacata  TA-rich tract