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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtactcttcacctcttccattcccatcagcgcgccgtcctcgcatcacatccatccctctcgtcttccccacag

Basic information

species Zea mays
transcript GRMZM2G059282_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 5'ss of exon 1
GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtactcttcacctcttccattcccatcagcgcgccgtcctcgcatcacatccatccctctcgtcttccccacag---------------
||| | ||||||||||||||||||||||||||||| ||||| || |||| |||||||||||||||||||||||| ||||||||||||||||| ||||| ||| | | | | | ||| | ||| || || | | ||| | | | || | | | | ||| |
GGCTTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAGTTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACGCTCCGCAACATGCTCACCTCCCCCGgttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgccttgaattatccaccaaatccaaatccaacacag

upper sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 1
GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtactcttcacctcttc-cattcccatcagcgcgccgt----cctcgcatcacatccatccctctcgtcttccccacag----------------
| | ||| ||||| |||||||| ||||||||||||||||| | |||| || ||| |||||||| || | ||| |||| ||||||||||| || || |||| | | || | ||| | | || || | | | | | | | | | | | |
GACACTGTGAAGCTGATCAGCGCAGAGGGCTTCGAATTCGTGATCGACAAGAGGGCTGCCATGGTTTCTCAGACCATCCGGAACATGCTCACTTCTCCCGgtatatttccgtttttattttctcgagacgattaggctactagaaaacgtaggaaaaaggaaagaaattaaattcttgaatcggaggtttattttattta
















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|211141709|gb|FL287346.1|FL287346
EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
EST: gi|211468741|gb|FL385438.1|FL385438
EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAKGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
EST: gi|13490768|gb|BG517532.1|BG517532
EST:     AAGGCCGCCATGGTCTCCAATATTCTTTCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: AAGGCCGCCATGGTCTCCAACA-CCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
EST: gi|61119394|gb|DN560355.1|DN560355
EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GTGGCTTTTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
EST: gi|211141707|gb|FL287344.1|FL287344
EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
EST: gi|211491482|gb|FL425975.1|FL425975
EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
EST: gi|18163997|gb|BM333836.1|BM333836
EST:     GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAG                         GCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCA

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: 178

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 542

GGCGTTGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTTGTTGACAGGAAGGCCGCCATGGTCTCCAACACCCTCCGCAACATGCTCACATCCCCAGgtagggtact ... ttccccacagGCGGCTTCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTA