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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctgtttgatgttctccatcttaattgatatttcaagttttaggtatctcataattcaactttctttgatacag

Basic information

species Zea mays
transcript GRMZM2G324540_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 4
AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtacc--------agctgtttgatgttctccatcttaattgatatttcaagttttaggtatctcataattcaactttctttgatacag
 ||||||| || |||||||||||||||||||||||||||||||||||||| ||  | ||||||||||| ||| |||||||||| ||||| || ||||||||||||          |||||||| ||| |  |  | ||||  ||  |  | ||| ||   ||||||| |||  | || || ||| |||
CGAGATGAAGCCAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCATCGATGGCAGGAGCTGCACCTACAGCTGTTGTCTCCAACGGGAAAAGAGgtacctactttctgactgtttgaagttgttgaagtaaatttctacatataatttcagccttctcatagttctgcattgttggattcag
















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|211040670|gb|FL334591.1|FL334591
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATC
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATC
EST: gi|211158673|gb|FL319015.1|FL319015
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
EST: gi|211165501|gb|FL341377.1|FL341377
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAA
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAA
EST: gi|211444525|gb|FL325223.1|FL325223
EST:     TCAGTTGCAGGAGCTGCTCCTGGCA-CTGTTGTTTCCAATGGAAAA-GAG                         TAATTGGAGATAAAAT-GGCCCTGACCGGAAAAAGATCCGTTCTGG
genomic: TCAGTTGCAGGAGCTGCTCCTG-CAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGG
EST: gi|211125236|gb|FL005609.1|FL005609
EST:     TGTTGTTTTCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
genomic: TGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
EST: gi|60400048|gb|DN232855.1|DN232855
EST:     GTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
genomic: GTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
EST: gi|148945896|gb|EC891188.2|EC891188
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
EST: gi|67020062|gb|CO448811.1|CO448811
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGA-                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAAATCCGTCCTGGTATCA
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctgtttgatgttctccatcttaattgatatttcaagttttaggtatctcataattcaactttctttgatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT