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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttctgtcacaatgttccttttgatttattgcatttccttctctcttatcaattactgtgggttctaaattcttgcttgatgattgcag

Basic information

species Zea mays
transcript GRMZM2G060045_T01
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os05g01700.1 (Oryza sativa), 5'ss of exon 21
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttctgtcacaatgttccttttgatttattgcatttccttctctcttatcaattactgtgggttctaaattcttgcttgatgattgcag
|| |||||||||||||| |||||||| |||||||| || ||||| ||||| ||||| ||| |  | ||  |  ||  ||   |||| ||   |||  ||    || || ||||| || || | |||||   |   |     |||||||
GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAAgtatgtgctgagccatgactttgattgacatttcttctctttatttg---ctgataaattagtgcggttcctaaaagatacttc----attgcag

upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: GLYMA18G02110.1 (Glycine max), 5'ss of exon 26
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgt---tctgtcacaa--tgttccttttgattt----------attgcatttccttctctcttatcaattactgtgggttctaaat-tcttgcttga-----tgattgcag
|| || ||||| |||||| | ||||| |||||||||||||||||||| |||||||| || |   ||| | |  |  | | ||||||  | |          ||||  |     | | | || |   |||   | | || ||| | |||||    |     |||| ||||
GCACGCTTGTTCTTCCATAAGCCTAAATTTGGTATCCTGGACGAGTGTACCAAgtatgtatgaatctatgattacttatgcctttttttctctcacttggaattgtttgcttctttttttttttggttaaccttgtttttaactgtcttgaaaaaaatattgatggcag

upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: GLYMA11G38160.1 (Glycine max), 5'ss of exon 25
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgt---tctgt-----cacaatgttccttttgatttattgcat-----------ttccttctctcttatcaattactgtgggttctaaattcttgc-----ttgatgattgcag
|| || ||||| |||||| | ||||| |||||||||||||||||||| |||||||| || |   ||| |     |  | | | ||||||  | | |  | |            |  || | | || |   |||   | | || ||   |||||      ||  |||| ||||
GCACGCTTGTTCTTCCATAAGCCTAAATTTGGTATCCTGGACGAGTGTACCAAgtatgtttgaatctatgattacgtattatgcctttttttctctcacgtggaattgtttgcttttttttttttttttgttaaccttgtttttactgtcttgaaaaaattattgatggcag

upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: PP1S150_142V6.1 (Physcomitrella patens), 5'ss of exon 25
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttctgtcacaatgttccttttgatt--tattgcatttccttctctcttatcaattactgt-gggttctaaat-tcttgcttgatg-attgcag
|| ||  | || ||||||||||| |||||||| || || |||||||||||||||||  |    |    || | |||  ||| ||    |    ||| | || |   |    ||  | | | |  ||||   | | ||   | |||   | |||
GCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAAgtaaattccatcatccatttttctatttaatcaccacaaaattactttttgcatggaaaaacattattgaattctgcgtatgttttctcatgcggttcag

upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: PP1S105_6V6.1 (Physcomitrella patens), 5'ss of exon 27
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttctgtcacaatgttccttttgatttattgcatttccttctctcttatcaattactgtgggttctaaattcttgcttgatgattgcag-------
|| ||  |||| ||||| |||||||||||||| || || ||||||||||| |||||  |||||     | || ||| | |  |  |  |  |||      |      | |   | ||   || | |   ||  |  | || |||| |        
GCACGACTGTTCTTCCACCATCCTAAGTTTGGGATTCTTGACGAGTGCACGAAgta-atgttcaccgcccattttcttctgtacattatttattaagacttaaagagttatccattgcaagtcc-atgctcgggagtaattattgaattttcgtc

upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: EFJ22756 (Selaginella moellendorffii), 5'ss of exon 24
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttctgtcacaatgttccttttgatttattgcatttccttctctcttatcaattactgtgggttctaaattcttgcttgatgattgcag
|| ||  | || ||||||||||| |||||||| || |||||||| ||||||||||| |    || | | | | || |      ||| |  ||   ||   || | |  | || || |                               
GCGCGACTCTTCTTCCATCATCCGAAGTTTGGAATTCTGGACGAATGCACCAAgtaag----ctcttaaagtctttccagccgtttttctca---ccaagtcccatg-cgataacag-------------------------------

upper sequence: GRMZM2G060045_T01 (Zea mays), 5'ss of exon 23
lower sequence: EFJ33165 (Selaginella moellendorffii), 5'ss of exon 23
GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttctgtcacaatgttccttttgatttattgcatttccttctctcttatcaattactgtgggttctaaattcttgcttgatgattgcag
|| ||  | || ||||||||||| |||||||| || |||||||| ||||||||||| |       ||  || ||  ||   |   | || | |  ||   || | |  | || || |                               
GCGCGACTCTTCTTCCATCATCCGAAGTTTGGAATTCTGGACGAATGCACCAAgtaagc------tcttaaagtctctccagccgt-tttcctcaccaagtcccatg-cgataacag-------------------------------

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|60345941|gb|DN212914.1|DN212914
EST:     CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
EST: gi|60351696|gb|DN218669.1|DN218669
EST:     CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
EST: gi|5714071|gb|AI944056.1|AI944056
EST:     GGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: GGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
EST: gi|60342685|gb|DN209658.1|DN209658
EST:     CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
EST: gi|32826847|gb|CD966525.1|CD966525
EST:     CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
EST: gi|211295643|gb|FL223363.1|FL223363
EST:     CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTAC
genomic: CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTAC
EST: gi|4646961|gb|AI622036.1|AI622036
EST:     TCCATCATCCTAAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: TCCATCATCCT-AAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
EST: gi|76292548|gb|DV032116.1|DV032116
EST:     CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA                         TGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT
genomic: CGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 38

GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCATGGGCATAACTGTGATCACTTCCTCTCAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 42

GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCATGGGCATAACTGTGATCACTTCCTCTCAA


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 13

GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCATGGGCATAACTGTGATCACTTCCTCTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAAgtacgtgttc ... atgattgcagTGCTACGAGTGTTGATGTCGAAGAGCATCTGTACAGACTTGCAACTAGCATGGGCATAACTGTGATCACTTCCTCTCAA