Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttactatacaaatcagtatgaaactgaattatctggtttttattgtagtatttcacttaggtagtaactaatagctccttcccctctttttttataaaaataaatgatcttgtacag

Basic information

species Zea mays
transcript GRMZM2G155836_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 5'ss of exon 4
ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttactatacaaatcagtatgaaactgaattatctggtttttattgtagtatttcacttaggtagtaactaatagctccttcccctctttttttataaaaataaatgatcttgtacag
|||||||| |||||||| ||||| || ||||||||||| ||||| ||||| |||||||||||||||   || ||| |||  | |       | || |   || | |    | || | |   |  ||| |  | | ||    |||||   ||||              |||||||||||| ||
ACCATTAGCTACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgt---tctggtggcgattgatgaacccttcatttctt-------------gaatgatcttgtatag
















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|149089860|gb|EE179141.2|EE179141
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|71315008|gb|DR794124.1|DR794124
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|87154289|gb|DY399078.1|DY399078
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|149111565|gb|EE190699.2|EE190699
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|89253101|gb|DY624887.1|DY624887
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|211396327|gb|FL436147.1|FL436147
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|76927490|gb|DV171263.1|DV171263
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|21390766|gb|BQ528815.1|BQ528815
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|148971909|gb|EE022686.2|EE022686
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|148932063|gb|EC875411.2|EC875411
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|149009140|gb|EE041278.2|EE041278
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|26455258|gb|CA826841.1|CA826841
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|149078458|gb|EE167238.2|EE167238
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|6626369|gb|AW257901.1|AW257901
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|148961324|gb|EE012052.2|EE012052
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|60401199|gb|DN234006.1|DN234006
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAC
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|5566821|gb|AI881687.1|AI881687
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|74234442|gb|DT642356.1|DT642356
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|149095924|gb|EE181586.2|EE181586
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
EST: gi|71446043|gb|DR827093.1|DR827093
EST:     ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAG                         GCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA
genomic: ACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 186

ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 158

ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 171

ACCATTAGTTACATGGCTGAGCGGGTGGTAGGTCATGGGTCCTTCGGAACCGTTTTCCAGgtttgttact ... tcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC