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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgtaccatgattgagagcacatgaattgatattcagtaagaaaattcacctattggctgctattaaaactgtag

Basic information

species Zea mays
transcript GRMZM2G069008_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069008_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g03910.1 (Oryza sativa), 5'ss of exon 3
GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgt-acca-tgattgaga---gcacatgaattgatattcagtaagaaaattcacctattggctgctattaaaactgtag
 ||||||||||||| |||||||||||||| || |||||||||||||||||||||||||| || ||  |||| || ||||| ||||| ||||||||||  | | | || | | || ||   || |||    || |||| || |       |    ||| | | ||| | |||| | |||
ATTCCAGGAATTGTATTTGCAAGAGGGCCTGCTGTTGCTGTGTTGATTCTTTTGGAGTCTAAAGGGCAAACTTACGCTGTTCTTACAGAACAGgtatgttatcatcagttactgtgaatggctcatattctggtatt-agaaccttgtgttgagtatcgaccgctctgaaaattttag
















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|149074765|gb|EE163195.2|EE163195
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATTTGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
EST: gi|71311098|gb|DR791863.1|DR791863
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
EST: gi|6021120|gb|AW066048.1|AW066048
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGNGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
EST: gi|148991430|gb|EE032932.2|EE032932
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
EST: gi|211274440|gb|FL232532.1|FL232532
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTG
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTG
EST: gi|148942503|gb|EC887518.2|EC887518
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
EST: gi|67016855|gb|CO445604.1|CO445604
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
EST: gi|76926121|gb|DV170728.1|DV170728
EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgtaccatgattgagagcacatgaattgatattcagtaagaaaattcacctattggctgctattaaaactgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG