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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttgtaggccatgtttgtggtgactagcactcaatgtgcttttctaatttgaattatgtggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT

Basic information

species Zea mays
transcript GRMZM2G075900_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 13
---------------gtgagtcttgtag-gccatgtttgtggtgactagcactcaatgtgcttttctaatttg--aatta--tgtggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT
                || |  || | |     |  || | | |    | |||   | |  |||   |||  |  ||  |    |||| ||||||  || ||||||| || ||||| ||| | ||||| | ||||||||||||||| |||||||||||| | |||||||||||||| || ||| ||||||||||
gtaagttctatagatatgggggttattgcatttttgttctagcgttgggtacttttttttttttgaaaatggggaaaccaatcatggtttgcagGTATTATCTTCCGTATGTTGGGTCACGCTACTGGCCGGCCTCTTCTTGGAGCCAAAGTTGTAGCCGCTATGCTTATGTTTGCAACTGTTTCTGGTATTCT

upper sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgagtct-------tgtaggccatgtttgtgg--tgactagcactca-atgtgcttttctaatttgaattatgtg--gtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT
|||||||        ||| ||  | |   |||    ||  |  |  || |  |      | ||       ||| ||  |||  ||||  |||| |||||||| |||||  ||| |||||| || ||| | |||||||||||||| |||||  | ||||| ||||||||||| ||   ||||||  |
gtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
















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|211464182|gb|FL297433.1|FL297433
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211461668|gb|FL297429.1|FL297429
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211253087|gb|FL453188.1|FL453188
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211464187|gb|FL297438.1|FL297438
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211461670|gb|FL297431.1|FL297431
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211464186|gb|FL297437.1|FL297437
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211464184|gb|FL297435.1|FL297435
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211461666|gb|FL297427.1|FL297427
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211461665|gb|FL297426.1|FL297426
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211464181|gb|FL297432.1|FL297432
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211464185|gb|FL297436.1|FL297436
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211464183|gb|FL297434.1|FL297434
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|60349341|gb|DN216314.1|DN216314
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
EST: gi|211461667|gb|FL297428.1|FL297428
EST:     AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTG                         GCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG
genomic: AGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 127

AAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

AAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT


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

AAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 149

AAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtcttg ... tggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtggtgactagcactcaatgtgcttttctaatttgaattatgtggtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT
                            ttctaat  putative branch site (score: 149)
                          ttttctaatttgaatt  TA-rich tract