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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtcgctgataatctattttttattgagcattcatctttgttggattctgtcatactcgtagctagcagttcatcttgaacctgtacataatcgtttctgtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 13
gtgagtgtcgctgataatctattttttattgagcattcatctttgttggattctgtcatactcgtagctagcagttcatcttgaacctgtacataatcgtttctgtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG
|||||| |   ||||| | | ||| ||     |  ||| |||||||| |  | |               ||||||  | ||||||  || |||| |||  | |       |||||||||||||||||||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||||||||||
gtgagtataa-tgatattatttttcttcacttg-gttcgtctttgttagccttt--------------cagcagtataacttgaatttg-acatgatcactcccac-cacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGACGAACTCTTTAAAGCAGCCAAG

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------------gtgagtgtcgctgataatctattttttattgag----cattcatctttgttg--gattctgtcatactcgtagctagcagtt-catcttgaacctgtacataatc-gtttctgtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG
                                                |   | | | | |||  |||      | | |      || |||  ||  ||  ||  ||   | || | |   | | |  |   |||||| ||  | |||  |    |  | | | |||||||||| || || || ||||| ||||| || ||| | ||||||||||| || ||||| |||||||||||||||
gtaggatttcattgattagtgattactattgaatctagctcgtagcctttgatattgataatatcctacagcgaaatcaagtcatatacatagttcctgctgaaactactaaacgcattatttgtatctgtttcttgatcccctgcatgttttaatggtatctctgcagGACATAAAATTGGCAGTTCATGCACATCCAACACTCTCTGAGGTCCTCGACGAACTGTTCAAAGCAGCCAAG

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------gtgagtgtcgctgataatctattt---tttattgagc-attcatctttgttggattctgtcatactcgtagc-tagcagtt--catcttgaacctgtacataatcgttt-----ctgtat---ttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG
                                        |  |||    |  | |  || |||   | ||| |    ||||||  |  || || ||  |   | ||  |   ||   |||   || ||    |  | | | ||| ||      | ||      |||||||||| |||||||||||||| ||||| || || ||||| ||||| || || |||||||||||| | || |||
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaa-atcctctttacatctatggcatgattcattatgttttgactc-ataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG

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|32944152|gb|CF048971.1|CF048971
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|67029833|gb|CO458582.1|CO458582
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|211287326|gb|FL348627.1|FL348627
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|13315813|gb|BG410365.1|BG410365
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|24767210|gb|CA402354.1|CA402354
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|16378693|gb|BI992557.1|BI992557
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|24769965|gb|CA405094.1|CA405094
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|31362407|gb|CD446764.1|CD446764
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|78075765|gb|DV504199.1|DV504199
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|211284887|gb|FL322128.1|FL322128
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|4885872|gb|AI676992.1|AI676992
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|60340265|gb|DN207238.1|DN207238
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|67018763|gb|CO447512.1|CO447512
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAA                         GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT
genomic: ATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGAT

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: 182

TGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

TGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

TGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcg ... gtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcgtagctagcagttcatcttgaacctgtacataatcgtttctgtatttgcagGACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG
                                        tttctgt  CT-rich tract
                              tacataat  TA-rich tract