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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcccacagccttatttgtcagaaataatctattcatactggatagtcgtgctgggctttgctaaattgttgatccagccttgtttgaataacg...

Basic information

species Zea mays
transcript GRMZM2G142984_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142984_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g38620.2 (Oryza sativa), 5'ss of exon 8
GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcccacagcctt-atttgtcagaaataatctattcatactggatagtcgtgctgggctttgctaaattgttgatccagccttgtttgaataacg---
 |||||||| |||||||||||||| ||||| ||||||||||||||| |||||| |  |||||  | |||   || |||| |||||| | ||| || | ||    | |    ||  |  ||  || |  |  ||  | | |  |    
TGTTGAAATCCATATTGGTGGTGCAAAGGGACCTCCAGACAGGgtaagtttcctagggcctttgtctgttgtaattaatatattca-attggttactggt--cagtccacactccacagtc-atgcttcactgacttactggctcca
















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|211320745|gb|FL468785.1|FL468785
EST:     GGTTGAAATMCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|17921527|gb|BM259178.1|BM259178
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|166530774|gb|EG240201.1|EG240201
EST:     TAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: TAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|149107225|gb|EE189109.2|EE189109
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGCCAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|32859979|gb|CD999660.1|CD999660
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|16926376|gb|BM079444.1|BM079444
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|5070005|gb|AI737970.1|AI737970
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|211383190|gb|FL437263.1|FL437263
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|67015787|gb|CO444536.1|CO444536
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|91867738|gb|EB399776.1|EB399776
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|17921853|gb|BM259489.1|BM259489
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|60344970|gb|DN211943.1|DN211943
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|116819630|gb|EC862778.1|EC862778
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCATACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|113837431|gb|DW959769.1|DW959769
EST:     CTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: CTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|91052774|gb|EB163192.1|EB163192
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGCCAGG                         GTGTTCATCTTTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|37392421|gb|CF633460.1|CF633460
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|111189956|gb|EE288092.1|EE288092
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|16918764|gb|BM073885.1|BM073885
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|87298726|gb|DY470729.1|DY470729
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|110531048|gb|EE035232.1|EE035232
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGCCAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
EST: gi|74035099|gb|DT535589.1|DT535589
EST:     GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG                         GTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT
genomic: GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcc ... ctaaatgtagGTGTTCATCATTGGACCAGAGAAGGAGGTCAGGAAAGCTGAGGCCATCTTT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGgtatgtttcccacagccttatttgtcagaaataatctattcatactggatagtcgtgctgggctttgctaaattgttgatccagccttgtttgaataacg

- - - - - - -  TGGTGG