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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttccattgctgagactactatttttttcttacctctgttggattacttatgaacaaattgttcaaagcttcaaaccagttgcagacttgcagtg...

Basic information

species Zea mays
transcript GRMZM2G042027_T05
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 5'ss of exon 8
GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttccattgctgagactactatttttttcttacctctgttggattacttatgaacaaattgttcaaagcttcaaaccagtt--gcagacttgcagtg-----
|| ||||| || ||| ||||||||||||| || ||||||||||| || ||||| || |||||||||||||||||||| |||||| ||||||||||    |||  || || || || | ||  |   | |  | ||  | | ||  | | |||    | | | || ||| || |  |    | |  || ||       
GGATATGGATCATTTTTACTTCGAGATCTGCCTTTTGATGCCATTCAATTCTGTATATATGAGCAACTTCGAATTGGTTACAAAGTTGTGgtacc----cat--cttagcct-ctgtcttgatgagaaccatattttacttctggttagcaatccttactaggcctcagacgacctcaatataaatgtaggattgag

upper sequence: GRMZM2G042027_T05 (Zea mays), 5'ss of exon 8
lower sequence: PP1S450_16V6.1 (Physcomitrella patens), 5'ss of exon 9
GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgta--ccgttccattgctgagactactatttttttcttacctctgttggattacttatgaacaaattgttcaaagcttcaaaccagttgcaga-cttgcagtg--------------------------------------------------------------------------------------
|||| ||| || || || ||||||||| ||||||||||||| |||||||| |||||||| ||||| ||| || | ||||  ||    ||||||         || | |     |   |   ||     || |||||      ||   | |  |  |||||  ||   | ||   |     ||| ||   ||||                                                                                      
GGTTTTGGATCTTTCCTCCTTCGAGATTTACCATTTGATGCTATCCAGTTTTGCATTTACGAGCAGCTTAGATTGGGCTTGAAGAAAGTGgtaagttaacttatggatagctttttcaaggttggaacacatctgtatacgcaca-gttacgattttgttttaaatcttaagagaagaatagaactaaaagtgtgtgtcatcaccgggctgttctatgtatttatagttgctctcagaggagttgacgttgaattaatgcttgtttttcactctttcag

upper sequence: GRMZM2G042027_T05 (Zea mays), 5'ss of exon 8
lower sequence: PP1S139_9V6.1 (Physcomitrella patens), 5'ss of exon 9
GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTA--CAAACTTGTGgtaccgttccattgctgagac-tactatttttttcttacctctgttgga----ttacttatgaacaaattgtt--caaagcttcaaaccagttgcagacttgcagtg
|| | | |||| ||  |  | ||||| ||||||||||||||  ||||||| ||||| ||||||||| |    ||  | ||  ||||   |  || |  |||  |  ||  ||  ||   ||      |||    | |  ||    | |  | |    ||||| ||  ||| |  |         | ||   ||  ||  
GGCTTTCGTTCATTCTTGTTACGAGACCTACCATTTGATGCATTCCAGTTTTGCATCTATGAGCAATTAAAGATCAGTTATGCAAAACGGgtgtgcacttctttcactctgaaatagggttcaacaattattcgtatgcgaaaattgatctttacgtaaatttttaacaagggatgtctttgtcttcaactttttag--

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|28984641|gb|BQ539144.2|BQ539144
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|113702185|gb|EE679689.1|EE679689
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|91056577|gb|EB166995.1|EB166995
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|16918359|gb|BM073712.1|BM073712
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|71302081|gb|DR787128.1|DR787128
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|78092776|gb|DV521150.1|DV521150
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|33092443|gb|CF052437.1|CF052437
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|113702087|gb|EE679591.1|EE679591
EST:     TGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: TGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT

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: 85

GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 57

GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG


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

GGTTATGGTTCCTTTCTACTTCGAGATCTACCATTTGATGCCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG