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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtaaactttatgcattattggtcagcatctgaacataatcatttgatgtaatctttacaattaactcctatgttaatattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 8
ttggtaaactttatgcattattggtcagcatctgaacataat-catttgatgtaatctttacaa--ttaactcctatgttaa--tattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT
     ||  | | |||   | |    |   ||| |   | || |     ||||  |  |||  |  | || | | ||  |||  ||||      || |||   |||||||||||||||||||||| ||||| ||||| ||||| |||||||||||| | ||||||||||||||||||||||| |||||||||||||| || ||||
-----aagttatttgctcaaatatctaatttctaattgttatgccaaaaatgttcttattatgaactaaattgccatactaaactatttcttacttgattttaagGTTTGGCGTATACGAACTGGCCAGTGTTTGCGTCGCCTCGAGCGTGCACATGCAAAAGGTGTTACAAGTGTTACATTCTCACGTGATGGAACTCAGATAT

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 9
-ttggtaaactttatgcattattggtcagcatctgaacataatcatttgatgtaatctttacaattaactcctatgttaatattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT
 |||       | |     | ||  |    || |  |  |  |||  | |     |   ||     ||||   |   |     | || ||||   |   |||| ||||||||  | ||||||||||||||||| || ||||| ||||| |||||  ||||||| ||||||||| | || || |||||||||| |||  |||
gttgtagttgctgacttgctgtttttggaaatgtttatgttttcacctca-actgttaatatgtaaaacttaaaaactgtatatttcacatttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 9
---ttggtaaactttatgcattattggtcagcatctgaacataatcatttgatgtaatctttacaattaactcctatgttaatattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT
   |||       | |     | ||  |    || |  |  |  |||  | |   | | || | |  |||  | ||      |||  || ||||   |   |||| ||||||||  | |||||||||||||| || || ||||| ||||| |||||  ||||||| ||||||||| | || || |||||||||| |||  |||
atgttgtagttgctgacttgctgtttttggaaatgtttatgttttcacctca---actgttaatatgtaaaacttaaaactgtatattcacatttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTACGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCCCGTGATGGAAGCCAGTTAT

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 9
ttggtaaactttat-gcattattggtcag-catctgaacataatcatttgatgtaatctttacaattaactcctatgttaatattctcccat----taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT
         || ||   | | ||||| |  |||  ||  ||         ||   |  |||   || ||     | | | || |  |  ||     ||  |  ||||| ||||||||| | |||||||| ||||| || || ||||| |||||||||||  |||||||||||||| ||   || || || |||||||  || ||| 
------tctttcattatactgttggtgaaacattggagtattgcttcaaaattggaagtttgacatcaaaattgaagatgatttatttgcaaactatatgtatcagGTGTGGCGTATAAGGACTGGTCAATGCTTACGCCGACTTGAACGTGCACATTCCCAAGGTGTTACAAGTCTTGTTTTCTCTCGAGATGGAAGTCAGATAC

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|211525027|gb|FL310982.1|FL310982
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCKACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|211475898|gb|FL358552.1|FL358552
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|76010783|gb|DT937953.1|DT937953
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTG
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTG
EST: gi|67019283|gb|CO448032.1|CO448032
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|23357683|gb|BU645332.1|BU645332
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|111433444|gb|EE297761.1|EE297761
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|22521028|gb|BU079839.1|BU079839
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|211160334|gb|FL327726.1|FL327726
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|26457208|gb|CA828791.1|CA828791
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|91873183|gb|EB403140.1|EB403140
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
EST: gi|211277652|gb|FL322062.1|FL322062
EST:     GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG                         GTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT
genomic: GTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACAT

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), 47 (downstream exon)
Score: 129

GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT


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

GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 33

GAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAGgtgcccttgc ... taattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgtaatctttacaattaactcctatgttaatattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT
                                    ttctcccatt  CT-rich tract
      taatctttacaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtaaactttatgcattattggtcagcatctgaacataatcatttgatgtaatctttacaattaactcctatgttaatattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - atgcatt
- - - - - - - - - - - - - -gcatctg
- - - - - - - - - - - - - - - - - aacataa
- - - - - - - - - - - - - - - - - - - - - - tttgatg