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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgtgatgttgagttagtctttgtaatccaacaattcaattagcatcctgtactcatgattctcaatcacatggtgaaccttacagtggtgcttgtcgtgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG

Basic information

species Zea mays
transcript GRMZM2G407044_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 3
gtatgatgtgatgttgagttagtctttg--taatccaacaattcaat-tagc--atcctgtactcatgattctcaatcacatggtgaaccttacagtggtgcttgtcgtgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG
|||  ||||| |||||| ||  | ||||  || |  || || |   | |||   ||   | |      ||  |  | | ||    | ||   |||      |||||  ||| || ||||||||||||||||||||||||||| |||| |||||||||||||| || ||||| || |||||||| |||
gtaacatgtgctgttgacttgctatttgcatagtgtaaaaactttgtgtagtgaattaagcaacaggcatgttggaactcact-cgtactgcacaaaat--cttgttatgattgtcagGTCATGGTTTTAGTTGATATTTTCCGAGCGAAAGTTGTTGATATTTCGGAGAACACCCTTACCATCGAG
















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|148959834|gb|EE153063.2|EE153063
EST:     GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG                         GTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
EST: gi|149075260|gb|EE163764.2|EE163764
EST:     GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG                         GTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
EST: gi|149087824|gb|EE177122.2|EE177122
EST:     GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG                         GTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
EST: gi|33098451|gb|CF058411.1|CF058411
EST:     GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG                         GTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
EST: gi|78122764|gb|DV541148.1|DV541148
EST:     GAGAGCTGATGCTTATAAAACTAAGTGTTGAACCTGATCAGCGTCCTGAG                         GTCGTGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAA
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
EST: gi|71435773|gb|DR816823.1|DR816823
EST:     GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG                         GTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
EST: gi|148949305|gb|EC894756.2|EC894756
EST:     GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG                         GTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG
genomic: GAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAGgtatgatgtg ... tgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgattctcaatcacatggtgaaccttacagtggtgcttgtcgtgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG
                        accttac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgtgatgttgagttagtctttgtaatccaacaattcaattagcatcctgtactcatgattctcaatcacatggtgaaccttacagtggtgcttgtcgtgactgacagGTCATGGTTTTAGTTGATATTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA