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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacccctagccaccttgtttacttgcgggaactcatcactcgtatctaggctgacagaaacctttggacttgaaccttttttag

Basic information

species Zea mays
transcript GRMZM2G004932_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 5'ss of exon 4
GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacccctagccaccttgtttacttgcgggaactcatcactcgtatctaggctgacagaaacctttggacttgaaccttttttag
|| || |||||||||||||| ||||| || |||||||||||||||||||| |||||||||| |||| ||||  |   ||| |||  ||||  |   | ||||||||||| |    | |||| |||||||| |||||||||||||||||     
GTGGTCGTTCAGAAGAACAGCCGGCGGGGGGTTCACTTCCGTCGTGCTGGACCTCGTCAGAAGgtatgatatgct--gccccctcttttaactattgaaactcatcacttgcgcgtgggctaacagaaacatttggacttgaacctttag---
















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|213183718|gb|FM190236.1|FM190236
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211119333|gb|FL065968.1|FL065968
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|71433707|gb|DR814757.1|DR814757
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211119335|gb|FL065970.1|FL065970
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGNCTGCATTGTAAATTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211118534|gb|FL065953.1|FL065953
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGN
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211119328|gb|FL065963.1|FL065963
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAAG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211119329|gb|FL065964.1|FL065964
EST:     ANAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAA-GCCTGCATTGTAACTTG
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTG
EST: gi|211119337|gb|FL065972.1|FL065972
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTTGTCAGAGG                         GTTTATTTTGGCACCGATNAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211118532|gb|FL065951.1|FL065951
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211119330|gb|FL065965.1|FL065965
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAATGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
EST: gi|211273595|gb|FL065975.1|FL065975
EST:     AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGG                         GTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC
genomic: AGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGC

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: 47 (upstream exon), 41 (downstream exon)
Score: 157

GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGCCTGTGCCCTGGGCTTAACACTGTTATCAGGGAACTGGTGTGTGGCTTGT


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 184

GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGCCTGTGCCCTGGGCTTAACACTGTTATCAGGGAACTGGTGTGTGGCTTGT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 268

GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGCCTGTGCCCTGGGCTTAACACTGTTATCAGGGAACTGGTGTGTGGCTTGT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 79

GTTGTTGTTCAGAAGAACAGTCGGCGTGGTGTTCACTTCCGTCGTGCTGGGCCTCGTCAGAGGgtaagatacc ... ccttttttagGTTTATTTTGGCACCGATGAAGTGAAAGCCTGCATTGTAACTTGTGGAGGCCTGTGCCCTGGGCTTAACACTGTTATCAGGGAACTGGTGTGTGGCTTGT