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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccagcattaactttaaaatttaggtagcaatatttacgatgttgatatgcatttccacatcatgttaaactttcag

Basic information

species Zea mays
transcript GRMZM2G097421_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097421_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g35570.1 (Oryza sativa), 5'ss of exon 6
TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccagcattaactttaaaatttaggtagcaatatttacgatgttgatatgcatttccacatcatgttaaactttcag
|||||||||||||||||||||||||||||||||||| |||||| | ||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||| || | | | | |||    |||||||| ||  | |   |||||| || ||||| | ||||||||| |||||||||||
TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAAACTTGGTTATTTGCAACTGTTTCAGCTATATGCATAATTATCCAGTTAATTTACCTGAACAAGgtaca-cctgtagtcattttg---tttaggtaacagaaatattgatgttaatttgcatgttcacatcatgataaactttcag
















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|78118379|gb|DV536765.1|DV536765
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTNCA-TACTGCAGTTGTTTCTCCCATCTACTATGCGAT
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTT-CAATACTGCAGTTGTTTCTCCCATCTACTATGCGAT
EST: gi|149012854|gb|EE042696.2|EE042696
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCC
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCC
EST: gi|74236901|gb|DT644815.1|DT644815
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTTCA-TACTGCAGTTGTTTCTCCCATCTACTATGC
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTT-CAATACTGCAGTTGTTTCTCCCATCTACTATGC
EST: gi|78118378|gb|DV536764.1|DV536764
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|149101364|gb|EE187481.2|EE187481
EST:     AACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTTAC-TGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTTGTT-CTCCCATCTACTATGCGAT
genomic: AACTGTTTCAGCTACATGCATAATTATTCAGTTAATTT-ACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTT-GTTTCTCCCATCTACTATGCGAT
EST: gi|148951157|gb|EC896836.2|EC896836
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTTATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|40334623|gb|CK368693.1|CK368693
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|60349889|gb|DN216862.1|DN216862
EST:     ACATGCATAATTATTCAGTTAATTTACNTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: ACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|94478877|gb|EB707835.1|EB707835
EST:     CAACTGTCTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATGGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTGCTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|78123628|gb|DV542012.1|DV542012
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|74244190|gb|DT652104.1|DT652104
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|71416856|gb|DR803834.1|DR803834
EST:     AACTGTTTCAGCTACATGCATAATTATTTCAGT-AATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGGTGTTTCTCCCATCTACTATGCGATG
genomic: AACTGTTTCAGCTACATGCATAATTATT-CAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|78079715|gb|DV508127.1|DV508127
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|91050129|gb|EB160547.1|EB160547
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|149005297|gb|EE039846.2|EE039846
EST:     ACTGTTTCAGCTACATGCATAATAATTCAGTTAATTTA-CTGGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGAT
genomic: ACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCT-GAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGAT
EST: gi|148948891|gb|EC894305.2|EC894305
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTTCA-TACTGCCAGT-GTTTCTCCCATCTACTATGCGA
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTT-CAATACTGC-AGTTGTTTCTCCCATCTACTATGCGA
EST: gi|71416855|gb|DR803833.1|DR803833
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
EST: gi|71446399|gb|DR827449.1|DR827449
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATG
EST: gi|76012865|gb|DT940035.1|DT940035
EST:     CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAG
EST: gi|149070088|gb|EE158488.2|EE158488
EST:     CAACTGTTTCAGCTACAGGCATAATTATTCAGTTAATTTACCTGAACAAG                         GCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG
genomic: CAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATG

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: 47 (upstream exon), 48 (downstream exon)
Score: 98

TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccag ... aaactttcagGCATTGGATACTTTCAATACTGCAGTTGTTTCTCCCATCTACTATGCGATGTTTACATCCCTCACAATTTTGGCAAGTGCCATAATGTTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAATTGAGGGCATAAACCAGGCTGGCTATTTCCAGACTTGGCTGTTTGCAACTGTTTCAGCTACATGCATAATTATTCAGTTAATTTACCTGAACAAGgtacagccagcattaactttaaaatttaggtagcaatatttacgatgttgatatgcatttccacatcatgttaaactttcag

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