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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaacatggcagatcatctaaaatacattactcgcccttgagaagttcctagacatggtgctaaccttgtaagcgctgtcattttgtgttacag

Basic information

species Zea mays
transcript GRMZM2G128877_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca---tggcag-----atcatctaaaatacat---tactcgcccttg-agaagtt-----cct-----agacatggt-----gctaaccttgtaagcgctgtcattt-tgtgttacag
|||||||| |||||||||||||||||||| ||||| || ||||| ||||| || || || |||||||| ||||||||||| |||||||||||||| |||||| |  ||||       ||     ||| |  | |  | |     ||  |  ||   || | ||     |||     |  ||| ||      ||||| |   ||  | ||| |||| ||| | ||||
GGAATGGGAGGTGCTGCCATGTATGAACTCGTCCGTGTTGGGCACGATAATCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacag

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaacatggcagatcatctaaaatacattactcgcccttgagaagttcctagacatggtgctaaccttgtaagcgctgtcattttgtgttacag
|| |||| ||| ||||| ||||||||||| || || || || |||||||| ||||| || |||||||| ||||| || ||  |||| ||||| |||||||||  |     |  || | | | |  ||||  |||||  |     |  | || ||    |||       | |||    | |||  |||||         
GGCATGGCTGGGGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTCTCGAAGGGAATTCTGCTACCATCCAAGgtgcat----tttcataccgtgtgcaata--ttact-acttcaaactaattact---tatgagaaactcattg-gttctctgcaattttag-------

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 2
GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaacatggcagatcatctaaaatacattactcgcccttgagaagttcctagacatggtgctaaccttgtaag--cgctgtcattttgtgttacag
|| |||| ||||||||| ||||||||||| || || || || |||||||| ||||| || |||||||| ||||| || || ||||| ||||| |||||||||  |     |  || | | |||  |||         |    ||  || | | |   | |  ||| || ||  |  |  | |||  |||||         
GGCATGGCTGGTGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTCTCGAAGGGGATTCTGCTACCATCCAAGgtgcat----ttccataccttctctaat---------gtttctgcaaactgcat---ccttctgcgaaactcattcgttctctgcaattttag-------

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|33095058|gb|CF055052.1|CF055052
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
EST: gi|211154399|gb|FL123518.1|FL123518
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
EST: gi|211068799|gb|FL177887.1|FL177887
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
EST: gi|5525243|gb|AI861241.1|AI861241
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
EST: gi|20300551|gb|BQ163494.1|BQ163494
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACA-TCCA-G                         TTTATGAGGAA-CAGCTGG-CTGAT
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGAT
EST: gi|20300262|gb|BQ163205.1|BQ163205
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
EST: gi|149014926|gb|EE044655.2|EE044655
EST:     CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAG                         TTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA
genomic: CCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGA

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: 883

GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1465

GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGAGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 756

GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1510

GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaaca ... tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGAGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGCGTCGGGCATGATAACCTCATCGGGGAAATTATCCGTCTTGAGGGCGATTCAGCTACAATCCAAGgtatacaacatggcagatcatctaaaatacattactcgcccttgagaagttcctagacatggtgctaaccttgtaagcgctgtcattttgtgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT