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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACATGTGTTAGGGAAGCCGTCCAGGATGGGATACAACCGCCACAGGCGTGGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattggttctgtttcaactctaaattatattttacctcgtggtaattggatttttgccactcataatgttgtcttcttgttataattaacactgt...

Basic information

species Zea mays
transcript GRMZM2G114758_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114758_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g09920.1 (Oryza sativa), 5'ss of exon 1
TACATGTGTTAGGGAAGCCGTCCAGGATGGGATACAACCGCCACAGGCGTGGCCGGGGATCATCCTCA---TCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg----gttctgtttcaactctaa-attatattttacctcgtggtaattggatttttgccactcataatgttgtcttcttgttataattaacactgt-
| |  ||    ||  |||  | |  |||||||||||||||    || || ||||| ||||| |||||    ||||| ||||||||||||||||| |||||| ||||||||||     |  |  |||    ||||       ||| |   ||     ||    |   |  ||  |   |  | | ||      || | |||    |||| 
TGC-CGTCGCCGGCGAGC--TTCGCGATGGGATACAACCGG---AGACGCGGCCGTGGATCCTCCTCCTCCTCGTCGTCGCGCCGCACCAAGCAGGAAGCCGCGTGgtaattatagcgcgcgatttgctatctaccgccgaattatgtttccgtccaa---aaccctctccctttggagggctttcaaagatttttgattcctgctgtt
















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|78118561|gb|DV536945.1|DV536945
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|78118561|gb|DV536945.1|DV536945
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|78118561|gb|DV536945.1|DV536945
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|78118561|gb|DV536945.1|DV536945
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|20301530|gb|BQ164473.1|BQ164473
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|20301530|gb|BQ164473.1|BQ164473
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|26456351|gb|CA827934.1|CA827934
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-
EST: gi|26456351|gb|CA827934.1|CA827934
EST:     GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC                         G
genomic: GGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattg ... ttggtttcag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACATGTGTTAGGGAAGCCGTCCAGGATGGGATACAACCGCCACAGGCGTGGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCgtggtaattggttctgtttcaactctaaattatattttacctcgtggtaattggatttttgccactcataatgttgtcttcttgttataattaacactgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC