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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

Basic information

species Zea mays
transcript GRMZM2G063949_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
||| ||   |  ||  |||  |||| || ||   | |    ||||   |   ||| ||  | |||||| |||||| | |   ||||||  |||||||||||| || ||  | |||||| |||| ||||||||||| || ||||| |||||||| ||||| ||||| |||||||| || ||||||||     ||||||
gtatgtcaaccagtccctttctgagaataatatacct--ccattt---cgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
----gtaagtgttcttgttt----cttggtgaggatcattatcttaattatttatgcaccatgttcagtctt--ctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
    ||     || |  |||     ||| | | | |  |     |  || ||  |  |   | || | |  |   ||  || ||   |   |    |  || || ||||||| |||||  |||||||| | |||||||| ||||| ||||| || ||||| || ||||| || || ||||||||||| ||||| ||  |  ||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttctt-ttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 5
--------gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
         | | | ||  | || |||  ||  ||  | | | || ||  ||||  |    | || |   ||     ||  |    | |  |  | || | ||||||||| |||||  |||||||| | |||||||| || || || ||||| |||||||||||  | ||||| || |||||||| ||||||||  || ||||||
gtcagttacttacttttgctattgctttttgttga--agtttgttgatattttagccggagttttgaaaatttgttcaaattttctgttttcctttgtct-gcagAATCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatg---cacggta------ccaatggtttt--gcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
    |||   ||   | ||| |   ||   ||   ||||   | |||  |   |  ||  | || |  ||  |||   |    ||      ||| |  ||||  | ||||||| |||||  |||||||| | |||||||| ||||| || || || ||||| || ||||| || || ||||||||||| ||||||||  |  ||||||
----gtgagtttacattttgatttagac--tttgtttaagcttgtatatatgttactcgatatttttggataatgattctaaatattttctccattccttttctgtagAATCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgc-accatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
|| ||| | |||  || ||| |  |    | | | |  || ||||  || |   | || |   ||     || ||   | ||     |   | |||||||||| ||| |  |||||||| | |||||||| || || || ||||| |||||||||||||| ||||| || |||||||| ||||||||  |||||||||
gtcagt-tacttactt-ttgctatgttgaagtttttagatgattttagccagagttttgaaaatttgttcaaaattttctgttttcctttgtctgcagAATCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
|||||| | |  | ||  |    | || |    |  |  | ||   |||| |   || | | || |    |  |    |||      |  ||| |||||||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||||||  |||||||||| |||||||||||||||||  |  ||||||
gtaagtatacaggcttagtc-caatgacctgagttcttctcatggctgcagc---ttaacttttttgtttaactttttggt----gggtattttcagAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
||||||||||     ||   ||    | |   ||  ||    | | || |  || | ||  ||| | ||   |||||     | |    | || |||||||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||| || ||||||||||| |||||||| ||||||||  |  ||||||
gtaagtgttc--aaatccaagtatataacccaatgctag---tctgtgtat-atatgcaagctt-ttagttaatgcat--ctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttat-gcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgca---gAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
                 || ||    |    | || |||   ||  | | |   | ||   | |||| |  |        |  |   |  |    ||   ||| || || ||    |||||  | |||||||| ||||| || || || |||||||||||||| ||||| ||||||||||| ||||| ||  || ||||||
----------------gttagtttcaacatctgtcataacatttagtagtattttttttctttttcttactactgatcttgctctttttctcccacaatagAACCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
|| ||| |     | | |     |  ||   |   ||  |  | | |    ||| ||   |  |||| ||   ||| |  |  |  |      | |||| || || ||  | |||||  | |||||||| ||||| || || || |||||||||||||| || || ||||||||||| ||||| ||  || ||||||
gttagtttcaacatctgtcat--aacatggcttgtttggtagtatttttttcat-tttttttgtctctgatcttgctctttttc--tcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

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|22715502|gb|BU197799.1|BU197799
EST:     TTGATGGTCCTAGTGAAGGTCTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|109637685|gb|EC591230.1|EC591230
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTNTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAAAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|149086197|gb|EE175737.2|EE175737
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|6021071|gb|AW065999.1|AW065999
EST:     TGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGNTGATGGGGGTCAGTCTCAG
genomic: TGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTT-GGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|40337281|gb|CK371351.1|CK371351
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|60356652|gb|DN223625.1|DN223625
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|32868566|gb|CF008248.1|CF008248
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|67020590|gb|CO449339.1|CO449339
EST:     TGATGGTCCCTAGTGAAG-TGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAA
genomic: TGATGGTCC-TAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|67011006|gb|CO439755.1|CO439755
EST:     GATGGTCCTAGTGAAGGTGTGCCCCTCGG-TTT-GGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: GATGGTCCTAGTGAAGGTGTGCC--TCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|149086196|gb|EE175736.2|EE175736
EST:     GGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: GGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|31356398|gb|CD440755.1|CD440755
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|7137694|gb|AW499223.1|AW499223
EST:     TTGATGGTCCTAGTGAAGGTCTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|31355714|gb|CD440071.1|CD440071
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
EST: gi|211213926|gb|FL245933.1|FL245933
EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

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: 304

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 89

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 34

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 166

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT