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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgttgtgcctggtggaacacgtcccttcgcaccaactattttcgcttgatgatttttctttttgcttgatttgataatttcattcacctgatcaatacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCTTTTCTGCAAACACTTGCTAAGATAATTGAGGATCCCAAGGATCTTACAT

Basic information

species Zea mays
transcript GRMZM2G036534_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 3'ss of exon 5
gtaagtttg-ttgtgcctggtggaacacgtcccttcgcaccaactattttcgcttgatgatttttctttttgcttgatttgataatttcattcacctgatcaatacatgt-agGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCTTTTCTGCAAACACTTGCTAAGATAATTGAGGATCCCAAGGATCTTACAT
|||| |||  |  |  ||| ||  |||| | | ||| ||| | | | ||  |       | |||| |||| |||| ||||           |||||||| |||||||| | |||| |||||||| |||||||||||||||||||| |||||||| |||||||||||||||||||| ||| | ||||||||||||||||||||||| |||||||
gtaaatttaatcatagctg-tgccacactttctttctcacaagccaattatg------aagtttttttttggcttaattt----------ctcacctgaccaatacatcttagGTCAATGTTACTGCTGATCATCGGGTTATTTACGGAGCTGATCTTGCCGCTTTTCTGCAAACTCTTTCCAAGATAATTGAGGATCCCAAGGACCTTACAT
















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|6539042|gb|AW225181.1|AW225181
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|6865176|gb|AW360526.1|AW360526
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|78106198|gb|DV524616.1|DV524616
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|23357491|gb|BU645140.1|BU645140
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|24768304|gb|CA403433.1|CA403433
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|6448387|gb|AW181153.1|AW181153
EST:     AGTTGTTGGTACAAAAGACGGTAGCAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGGTATTTATGGAGCTGGCCTTGCCGCT
genomic: AGTTGTTGGTACAAAAGACGGTAG-AATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|211440164|gb|FL434174.1|FL434174
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|6022391|gb|AW067319.1|AW067319
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|71765103|gb|DR963040.1|DR963040
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|60344293|gb|DN211266.1|DN211266
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|78088435|gb|DV516828.1|DV516828
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCG
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCG
EST: gi|149027250|gb|EE046447.2|EE046447
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|93013412|gb|EB638932.1|EB638932
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|93284411|gb|EB676675.1|EB676675
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|83279414|gb|DV943422.1|DV943422
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|74246257|gb|DT654171.1|DT654171
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|78074314|gb|DV502748.1|DV502748
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|71759734|gb|DR957671.1|DR957671
EST:     CAGTTGTTGGTAC-AAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|74236968|gb|DT644882.1|DT644882
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
EST: gi|149035803|gb|EE155127.2|EE155127
EST:     CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG                         GTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT
genomic: CAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCT

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 3

GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAGgtaagtttgt ... atacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCTTTTCTGCAAACACTTGCTAAGATAATTGAGGATCCCAAGGATCTTACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttttctttttgcttgatttgataatttcattcacctgatcaatacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCTTTTCTGCAAACACTTGCTAAGATAATTGAGGATCCCAAGGATCTTACAT
                                    acctgat  putative branch site (score: 3)
                   atttgataatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgttgtgcctggtggaacacgtcccttcgcaccaactattttcgcttgatgatttttctttttgcttgatttgataatttcattcacctgatcaatacatgtagGTAAATGTTACCGCTGATCATCGGGTTATTTATGGAGCTGACCTTGCCGCTTTTCTGCAAACACTTGCTAAGATAATTGAGGATCCCAAGGATCTTACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT