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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC

Basic information

species Zea mays
transcript GRMZM2G470556_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 10
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttt-tgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
||||| | | ||   |||||| ||||| |    | |  ||||   |||  || ||||| |  | ||   |  | | || |  ||  |      || |  ||   ||| || |     ||||     | ||  ||   |       |  |||   |||| |||||||||||||||||||| || |||| ||| || |||||||| |||||||||||||| ||||||||||| || |||||||||||||| || || |||||||
gtaatgttctatgtttgctgagtttttcta---aatttaaatgcgttgttttgccaggctggtcatactatttttgtatgcaactctttgggggggattctgccttcctccttaggctagcgtttttctgcactatctaatgctaggtctctatgtgttcagATAGGATATCTTGAATATTGCAAGCAGCGTGGATTCACAAGCTGTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                               |     || ||| ||  | ||| ||   |     |||| | | | |    | ||||   |||| |  | ||   || || |     | || |||||||  |   |  | || |||| || || || |||||||| ||| |||| || ||||| || || |||||||||||||| || ||  ||||||| || ||||| ||||||||||| ||||
-----------------------------------------------gtaagtcctggtcttc-tgaaaccttggtgtttaacca-atatctgtg--ctttttactttctacactgtatggaggatctaa---gagtataatctgatc---ctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                                             | | |   | |   |  ||  | |                |||    |  || | | |||  ||   ||  |      |||  ||  |  | |  | ||||| || || ||||| |||||||||   || || ||  |||| || || |||||||| ||||| ||| | |||||||||||||| || |||||||||||||
------------------------------------------------------------gtaagccgcatttcttctgatccta-----------gttgctttcaggcacctgtgttgctt-cacaagtcttatcaacaatgggctttt-cggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcac-cgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                                                       |   | |  |    |  | |  |     | |  |||||| | ||  |   |     || |    |  || | | |||| |  | | | ||||| || ||||| |||||||| ||  |||| || ||||| || || |||||||||||||| |||||  |||||||||| ||||| ||| ||||||||||||
----------------------------------------------------------------------gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatgga-----tgattcaagggtattataccctgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 9
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagac-catacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                  ||  |  |||| |      |||   ||| ||  |  ||   |  |  |  | ||      | || ||||||   |     | || |||   ||          ||  ||   |  ||        ||||| |||||||| ||||||||||||  |||||| ||||||||||| || ||||||||||| || ||||||||||||||||| || || || ||||||||||
----------------------------------gtg-agttttagtattacgccaatcttttatttattcttgatgagcaattcttatggtttggaatctttttatattgggctattggcttatat---------atccgattctctttc--------cagATTGGATATCTCGAATACTGTAAGAAGCGGGGTTTCACAAGTTGCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 11
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatc-tgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                                          |||   | || | | |||   | |  |               |  | || ||  | ||  | | || | |    |     ||||  ||  |  ||  | | ||||| || ||| | || || |||  |  | | || || |  ||||||||||| |||||||||||||| || |||||||| ||||| || |||||||| ||||
---------------------------------------------------------atttgtgttaatattttctgtaatagaactttggttctgctgctgctgctactgttcttctgtttgcctat----taaacttaattgtgtacatact-tctgcagATTGGCTATTTAGACTATTGTCGGAGGAGAGGTTTTAGTAGTTGTTACATTTGGGCTTGCCCACCATTAAAGGGTGAGGATTATATTTTATATTGTCATC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S462_17V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacg-agaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                                               ||      | | |||  | |   ||   | |       | ||  | | |  |||   || |||       ||    |  |      | | |   | ||||| || ||||| || ||||||  |  | | || || |  || |||||||| ||||||||||||||| | ||||| || ||||| || |||||||| ||||
--------------------------------------------------------------aattttttttctttacttaaaatgtagtgctgctgtttctgttgttacgttgtttgtactggcagaccagttgaacttgttggcgtatgatctgttgcagATCGGCTATCTAGATTACTGTCGGAGGAGAGGTTTTAGTAGCTGTTACATTTGGGCTTGCCCACCTCTAAAGGGAGAGGATTATATTTTATATTGTCATC

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|211057050|gb|FL391369.1|FL391369
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGCCTGCGGGGGTTCACAAGTTGTTACAT
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGC-TGCGGGGGTTCACAAGTTGTTACAT
EST: gi|211363258|gb|FL387051.1|FL387051
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
EST: gi|211235994|gb|FL378061.1|FL378061
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGATTACTGTAAGNCTGCGGGGGTTCACAAGTTGTTACAT
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAG-CTGCGGGGGTTCACAAGTTGTTACAT
EST: gi|211022186|gb|FL381963.1|FL381963
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
EST: gi|211490473|gb|FL383680.1|FL383680
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
EST: gi|211539239|gb|FL396300.1|FL396300
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGCCTGCGGGGGGTCCCAAGTTGTTACAT
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGC-TGCGGGGGTTCACAAGTTGTTACAT
EST: gi|211179796|gb|FL384668.1|FL384668
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGNAAGCTGCGGGGGTTCACAAGTTGTTACATA
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
EST: gi|211153694|gb|FL418631.1|FL418631
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGGCTGCGGGGGTTCACAAGTTGTTACAT
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAG-CTGCGGGGGTTCACAAGTTGTTACAT
EST: gi|211046001|gb|FL422502.1|FL422502
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAAGCCTGCGGGGGTTCACAAGTTGTTACA
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAA-GC-TGCGGGGGTTCACAAGTTGTTACA
EST: gi|211343346|gb|FL378210.1|FL378210
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATA
EST: gi|211398119|gb|FL400636.1|FL400636
EST:     AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTG                         ATAGGATATCTTGAATACTG
genomic: AAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTG

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: 45 (upstream exon), 45 (downstream exon)
Score: 51

TGTTTATTTGTCATACTTGGATTCTGTTAAGTACTTTAGACCTGAGATTAAAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 62

TGTTTATTTGTCATACTTGGATTCTGTTAAGTACTTTAGACCTGAGATTAAAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

TGTTTATTTGTCATACTTGGATTCTGTTAAGTACTTTAGACCTGAGATTAAAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

TGTTTATTTGTCATACTTGGATTCTGTTAAGTACTTTAGACCTGAGATTAAAACAGTATCCGGAGAGGCCTTGCGTACATATGTATACCATGAAATTCTGgtaatttacc ... ccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
                                       ccctcac  putative branch site (score: 84)
                                       ccctcacc  CT-rich tract
      ttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA