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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttccatgttttgatatgttggatccttttatttagacgaattataacctttcatgtatatcatatgcag

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 7
GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttccatgttttgatatgttggatccttttatttagac---gaattataacctttcatgtatatcatatgcag
|| ||||||||||| |   | |||||||||||||||||||| || |||||||| || ||||| ||||||||||||||||| |||||  || ||||| ||| | || |||| |          |||    ||| ||||||  || |  |||| |||||||||
GTACTTGGAACAGAAGCACTAAATGCTTATTTGAACAAGTACCATATTGAGCTTGATCCTCAGCTTGAAGCTCTTGTTGGGAGgtacgttgccatgcttttagatattggttttgaacgggaagattcagaagtataacactt-acatata-catatgcag
















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|67025945|gb|CO454694.1|CO454694
EST:     A-CAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|71761092|gb|DR959029.1|DR959029
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|6095381|gb|AW120048.1|AW120048
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|149085357|gb|EE174864.2|EE174864
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|31998439|gb|CD662075.1|CD662075
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|149097606|gb|EE183499.2|EE183499
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|31997697|gb|CD661720.1|CD661720
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|60345677|gb|DN212650.1|DN212650
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|32839753|gb|CD979434.1|CD979434
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCACAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|5607774|gb|AI901441.1|AI901441
EST:     AGCTGG-CCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|32925412|gb|CF030224.1|CF030224
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCACAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|7216891|gb|AW563013.1|AW563013
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|71446426|gb|DR827476.1|DR827476
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|5525642|gb|AI861535.1|AI861535
EST:     AGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|110941068|gb|EE161225.1|EE161225
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|30705895|gb|CD058961.1|CD058961
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|14203981|gb|BG837658.1|BG837658
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|60340774|gb|DN207747.1|DN207747
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|30706066|gb|CD059017.1|CD059017
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|148929900|gb|EE285653.2|EE285653
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|5922209|gb|AW055479.1|AW055479
EST:     GCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCACCATCT
genomic: GCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|32870873|gb|CF010555.1|CF010555
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCACAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|30087041|gb|CB885249.1|CB885249
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|7135281|gb|AW498007.1|AW498007
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|18177159|gb|BM378369.1|BM378369
EST:     AGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|67020854|gb|CO449603.1|CO449603
EST:     AAC-AGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|19436338|gb|BM952748.1|BM952748
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCACAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
EST: gi|6095382|gb|AW120049.1|AW120049
EST:     AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG                         GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT
genomic: AACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCT

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: 274

GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttcc ... tcatatgcagGCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAGgtaaatttccatgttttgatatgttggatccttttatttagacgaattataacctttcatgtatatcatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG