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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttctgacttgtttcgttagcatattagcttattgtctttactagtggctgatttctttgtcataatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC

Basic information

species Zea mays
transcript GRMZM5G880300_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g34620.4 (Oryza sativa), 3'ss of exon 6
-------------------gcaagtttc-tgacttgtttcgttagcatattagcttattgtctttact-agtggctgatttctttgtcat--aatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC
| |||| | || | | || | |||| | |||| ||| ||| ||||| ||| | | ||| | |||||||||||| ||||||||||| | ||||| ||||||||||||| |||||||| | || ||| || | || |
gcaagtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaat-tcttaactcagtaattgattccttatttgtgtaattttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAAAA--CGAATCATCATGAAGAA-GATATA---------------------

upper sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g34620.7 (Oryza sativa), 3'ss of exon 6
---------------gcaagtttc-tgacttgtttcgttagcatattagcttattgtctttact-agtggctgatttctttgtcat--aatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC
| |||| | || | | || | |||| | |||| ||| ||| ||||| ||| | | ||| | |||||||||||| ||||||||||| | ||||| ||||||||||||| |||||||| | || ||| || |||| || | || | | ||
gtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaat-tcttaactcagtaattgattccttatttgtgtaattttcttcagaagGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAAAA--CGAATCATCATGAA----GAAGATATAGTACGCCATTTTTGTCAC

upper sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g34620.5 (Oryza sativa), 3'ss of exon 6
-------------------gcaagtttc-tgacttgtttcgttagcatattagcttattgtctttact-agtggctgatttctt--tgtcataatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC
| |||| | || | | || | |||| | |||| ||| ||| ||||| ||| | |||| | |||||||||||| ||||||||||| | ||||| ||||||||||||| |||||||| | || ||| || |||| || | || | | ||
gcaagtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaat-tcttaactcagtaattgattccttatttgtgtaattttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAAAA--CGAATCATCATGAA----GAAGATATAGTACGCCATTTTTGTCAC

upper sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g07950.1 (Oryza sativa), 3'ss of exon 6
-------------------gcaagtttc-tgacttgtttcgttagcatattagcttattgtc--tttactagtggctgatttctttgtcataatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC---------
|| |||| | || | | | || | | ||| | | | |||| | | || ||| ||||| | |||||||||||| ||||||||||| | ||||| ||||||||||||| | || ||||||| ||| |||||||| ||| |||| | ||||
gcaagtgagcttattgtccccaggttttattaccaggtgtatccatctacaatttaattcttaactcagtagttgattccttattttgtataattttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGCGATATTGCACAAAAGCATGAGCAAAAAGAA-----TCA----TCATGAAGATGACAATAGTACGCCATTTTGGTCACGTGAG

upper sequence: GRMZM5G880300_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g34620.8 (Oryza sativa), 3'ss of exon 5
-------------------gcaagtttc-tgacttgtttcgttagcatattagcttattgtctttact-agtggctgatttctttgtcat--aatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC
| |||| | || | | || | |||| | |||| ||| ||| ||||| ||| | | ||| | |||||||||||| ||||||||||| | ||||| ||||||||||||| |||||||| | | || || | | | | | | | |
gcaagtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaat-tcttaactcagtaattgattccttatttgtgtaattttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAAAACGAATCATCATGAAGAAGATATAGTACGCCATTTTTGTCACGTGAGC

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|74236784|gb|DT644698.1|DT644698
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|211479938|gb|FL425914.1|FL425914
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|91877551|gb|EB407508.1|EB407508
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCT
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCT
EST: gi|93017644|gb|EB643164.1|EB643164
EST:     TCANAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|76281315|gb|DV020883.1|DV020883
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|211328326|gb|FL186217.1|FL186217
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAR                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|84980275|gb|DW530624.1|DW530624
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|211069174|gb|FL417736.1|FL417736
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAANGATCTTCTTGGGGATATTGCACAA-GAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|101389214|gb|EB816562.1|EB816562
EST:     TCANAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|28984540|gb|BQ539134.2|BQ539134
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|93017643|gb|EB643163.1|EB643163
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|74236783|gb|DT644697.1|DT644697
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
EST: gi|84980198|gb|DW530547.1|DW530547
EST:     TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAG                         AAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAA

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: 41 (upstream exon), 49 (downstream exon)
Score: 62

TAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 89

TAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 50

TAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 83

TAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagtttct ... tctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattagcttattgtctttactagtggctgatttctttgtcataatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC
                         ggctgat  putative branch site (score: 83)
 tctccttc  putative PPT
 atttcttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtttctgacttgtttcgttagcatattagcttattgtctttactagtggctgatttctttgtcataatctccttcagAAGGGTGAGCTTAAGGATCTTCTTGGGGATATTGCACAAAGAGACGAACAAAAAGTGCATGCTCACGATTCATGAAGCAATCAACAGTAGGTTCTTTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA