Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgcaggctgtatctatttcaaattttaactgaagaaactggtttcttttaacttactagctatcgttatttgcgtgcag

Basic information

species Zea mays
transcript GRMZM5G883149_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 5
GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCT---TCATCGGCTGAGCAGgtaggctgcaggctgtatctatttcaaattttaactgaagaaact-ggtttcttttaactta-ctagctatcgttatttgcgtgcag
|||||| || |||||||||||||| | |||||||||||||||||| |  || |||   || ||||||   |||   |||||||||||| | |  || |   ||||        |  |||  ||||    | |||||     ||| || | || ||| | | | ||  |||||
GATTGTCCTGGAAACAGAAGGAAGTGTGATAGCTGAAAAGGTGTCAGCACATGGAATAGAAGGTGCTACTTCACTCGCTGAGCAGgtaagttttagccatgatct--------tactaaaggaagctgttcggtttaaccaaacataacgagttattgctctctgaatgcag
















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|67020825|gb|CO449574.1|CO449574
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|211335317|gb|FL100773.1|FL100773
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCC
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCC
EST: gi|60344091|gb|DN211064.1|DN211064
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|166429976|gb|EG169952.1|EG169952
EST:     GTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: GTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|32937965|gb|CF042784.1|CF042784
EST:     TTGAAAAGGTGCCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|50324980|gb|CO520106.1|CO520106
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|50324981|gb|CO520107.1|CO520107
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|211477574|gb|FL100774.1|FL100774
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGA
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGA
EST: gi|116827357|gb|EC871252.1|EC871252
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCGTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|40303119|gb|CK347506.1|CK347506
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|211529711|gb|FL481418.1|FL481418
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|166651131|gb|EG138260.1|EG138260
EST:     GAAAAGGTGCCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTC
genomic: GAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTC
EST: gi|5714079|gb|AI944064.1|AI944064
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
EST: gi|113703727|gb|EE681231.1|EE681231
EST:     CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAG                         ACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT
genomic: CTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgca ... ttgcgtgcagACTTTAGTCAATGCCCTAACGCAAGCAAGAGAGCATCTGGCGAAGTCTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCACGGATCGGAGGGTGCTTCATCGGCTGAGCAGgtaggctgcaggctgtatctatttcaaattttaactgaagaaactggtttcttttaacttactagctatcgttatttgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG