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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG

Basic information

species Zea mays
transcript GRMZM2G071154_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
gtacagtacagcacagcacagcacagtagccactagccagttcg-tggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG
                          ||    ||||| | |  | |  ||     | || |||  ||    |||   | |  |||    || ||   |   |  ||        ||    |||   |  | |  ||   |||| |||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| |||
-------------------------atattt-ctagcaactctgataatttttactactcgctaattacgagtttattatt-ttgtgaattattgcctaattacat--------acttatttc---tttttcattc---agGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG

upper sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 2
gtacagtacagcacagcacagcacagtagccactagccagttcg-tggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG----------------
                          ||    ||||| | |  | |  ||     | || |||  ||    |||   | |  |||    || ||   |   |  ||        ||    |||   |  | |  ||   |||| |||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| |||                
-------------------------atattt-ctagcaactctgataatttttactactcgctaattacgagtttattatt-ttgtgaattattgcctaattacat--------acttatttc---tttttcattc---agGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGGTACCATTGATCTTCA

upper sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttctt-----cttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG
||   |||   |     |     ||  | |        | ||| ||  | | |||      ||||        |      |  |  |     |||| |  || |   ||| ||| |  |||   |    || ||   ||   ||||| || ||||| || || || ||||| || || || || |||||||||||||||||||| ||||| || ||||| ||||| |||
gt-ttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttttggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgcaccattacctaatgtt-atacttgtatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG

upper sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG
                                                                | | |  | | || |   ||||||||   ||||  |    || |         |  ||      ||| ||  ||||||  | || || || ||  ||||||||||  | || |||||||||||||||||||||| ||| |||||| | || || || |||
---------------------------------------------------------------gtacgtattacact-taagtgcttctttgccgttgtcctctttgaaactctaaagaatctatcaatccaat--ccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

upper sequence: GRMZM2G071154_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgc-ttcttcttcgttcgctgtattcacgaggaccc----ggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG
                                                                            |   |||   |||||||| |  || |||  ||    | || |    |  ||      ||| ||  ||||||  | || || || ||  ||||||||||  | || |||||||||||||||||||||| ||| |||||| | || || || |||
--------------------------------------------------------------------gtacgtattacacttaagttcttctttgc-cgttgtcctctttggaactctaaagaatctatcaatccaat--ccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG

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|76018940|gb|DT946110.1|DT946110
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|149002886|gb|EE038882.2|EE038882
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTTGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|18178271|gb|BM379481.1|BM379481
EST:     CCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGAACCGACGGCGTGGGAGGACAAG
genomic: CCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|8367109|gb|BE050054.1|BE050054
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|50336543|gb|CO531669.1|CO531669
EST:     CCCTCTTCCTTTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|149082668|gb|EE171878.2|EE171878
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|60338891|gb|DN205864.1|DN205864
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|93015747|gb|EB641267.1|EB641267
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|149000689|gb|EE037900.2|EE037900
EST:     GCACCAGCTCCACGGCATCTTGGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: GCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|211386348|gb|FL456698.1|FL456698
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|9953961|gb|BE640544.1|BE640544
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|110517513|gb|EE022100.1|EE022100
EST:     CCCTCTTCCTTTACAACTACTCCACGCACCAGCTCCACGGCATCTTTGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|211074694|gb|FL076199.1|FL076199
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|78022808|gb|DV491195.1|DV491195
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|149088944|gb|EE178087.2|EE178087
EST:     CCCTCTTCCTCTACAATTACTCCACGCACCAGCTCCACGGCATCTTGGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|4730256|gb|AI649422.1|AI649422
EST:     GGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: GGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|149090354|gb|EE179660.2|EE179660
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTTGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|71444740|gb|DR825790.1|DR825790
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
EST: gi|211171601|gb|FL423137.1|FL423137
EST:     CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAG                         GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAG

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: 44 (upstream exon), 48 (downstream exon)
Score: 62

GCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

GCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 470

GCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

GCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtaca ... cgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG
                                        tcctcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccagGCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGACGGCG