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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG

Basic information

species Zea mays
transcript GRMZM2G166035_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 5
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgcc-gttactgttatttgtactgtttgattattcga--aatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
             | | ||  | | |     ||||  |||||| |   |  || |  || |   | ||| || || | | |   ||  |  | | || |||||| ||| | || ||||| ||||| ||||| |||||||||||||||||||| || ||||||| |||||| |||||||| || || ||||||
------------gtaatttcatgattcctttgaaattatctattttgctttgtacttgtaatgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 5
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgcc-gttactgttatttgtactgtttgattattcga--aatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG--------
             | | ||  | | |     ||||  |||||| |   |  || |  || |   | ||| || || | | |   ||  |  | | || |||||| ||| | || ||||| ||||| ||||| |||||||||||||||||||| || ||||||| |||||| |||||||| || || ||||||        
------------gtaatttcatgattcctttgaaattatctattttgctttgtacttgtaatgatcattggttctttctaacggttgaacgactttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGGTTTGACT

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 6
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
|||| |||        || ||  | | |         || |   | |     |   |||  |  | | | |     ||    |  | |  | |  ||| || |||||||| ||||| ||||| ||||| || || ||||||||||||| |||| |||||| ||||||||||||||| || |||||| ||
gtaa-ggtc-------atcttatagttagtttttgttatttgatttatagattcttgttgtttgtctctatggaaattttaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 5
gtaatggttcctctgaatttttcaataaaaaga-----------aaccatctatctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
||||||    | || |   ||   ||| |   |           |   |  ||  |||  |  |     ||   |  ||   ||| || ||| |      || |  ||| || |||||||| || || ||||| ||||| ||||| || |||||||||| |||| |||||| ||||||||||||||| || |||||  ||
gtaatgtcatcactcatcattaacatatagtcagctttagttttatttacttaattcaaaaaatatatatataatgcttatcactatt-gataacatcgcatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 5
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgccgttactgttatt-tgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
|||| | |  ||   | ||      |    |      || |||   |  |     | |   ||| | | || |   | | |  | |  |  | |  ||| || |||||||| ||||| ||||| ||||| || || ||||||||||||| |||| |||||| ||||||||||||||| || |||||| ||
gtaaggttatcttctagttagctttttgttatttg--atttattataagattcatcttgtttgtcactatggaaaatctaaacact--atgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
||||||    |  | |  | |                || ||| | | |       | || |  | ||| |     ||||| |    | || |  ||| || |||||||| || || ||||| ||||| ||||| ||||||||||||| |||| |||||| ||||||||||||||| || |||||  ||
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattctaaaaagata-taatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcag-tacgtgccgttactgttatttgtactgtttgattattcgaaatct-----gtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
                             |||||| ||| || || |  |   |    ||| |  |  || ||   |||| ||| | | |||         ||| ||||||||||| || || ||||| ||||| ||||| |||||||| ||||   | ||||||| ||||||||||||||| || || ||  ||
---------------------------gtaagaaaacatttaactgaaatttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG

upper sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 6
gtaatggttcc--tctgaatttttcaataaaaagaaaccatctatctcagtac---gtgccgttactgttatttgtactgtttgattattcgaaatc---tgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
|||| |    |  ||   |  |||    ||  |  || |||  | |  |||     |||   |     ||  ||| |   | | || |||  || ||   |  ||| || ||||| || || || ||||| ||||| ||||| ||||||||||||| ||||||||||| ||||||||||||||| || |||||| ||
gtaaggacatcaatcgttaggtttttccaagtattaatcatagaacaaagtttccagtgatttggtaattgcttgcatcttctaatgattgaaattcgtttacagGAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

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|19350739|gb|BM895271.1|BM895271
EST:     AGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGAGAGTGG
genomic: AGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGG
EST: gi|6826953|gb|AW330596.1|AW330596
EST:     AGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATA
genomic: AGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATA
EST: gi|31359010|gb|CD443367.1|CD443367
EST:     AGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGAGAGTGGGTGGCGTTCT
genomic: AGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGGGTGGCGTTCT

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: 330

CAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

CAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

CAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 346

CAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTGgtaatggttc ... aaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG
                                gtttgat  putative branch site (score: 346)
                                 tttgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggttcctctgaatttttcaataaaaagaaaccatctatctcagtacgtgccgttactgttatttgtactgtttgattattcgaaatctgtagGGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC