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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttcactcttcacactgtgttgttaaactggtacatatggaggaaaactgatcattgtgccagattcatgaaaagcttaatagtgtcttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT

Basic information

species Zea mays
transcript GRMZM2G131120_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g05650.1 (Oryza sativa), 3'ss of exon 3
cttcttcactcttcacactgtgttgttaaactggtacatatggaggaaaactgatcattgtgccagat---tcatgaaaagcttaatagtgtcttcttgac---------agATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT
            ||  |   |||  || | ||  | | |||||||  |  |   ||||| |||  | |   || ||||| | |  ||  |  |||||||           ||||||| ||||||||||| |||| || |||||||||||||||||||| || || |||||| ||||||| |||||| ||||||||||||||||||| |||||
----------aatctgaagttgtactttagctc-tgcgtatggagttactcgattcatt-tgctgggtttctcctgaaatgatcgatgttaccttcttgttttacttgcaagATAATCTGGTGGAGGATCTATTGAGTGATTTTGAATATGAACTTCAACCTCCGTATTTGTTGTACCGCAATGCTGCCCAAGAAGTAAATGGTATCTGGTT

upper sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G39120.1 (Glycine max), 3'ss of exon 3
cttcttcactcttcacactgtgttgttaaactggtacatatggaggaaa--actgatcat-tgtgccagattcatgaaaagcttaatagtgtcttcttga-cagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT
    |  |    |       | ||  || ||| ||   |   ||   |   | ||  |||   ||  |  | |||   |  |||     ||    | | | |||| |||||||||||| || | ||  |||||||||| |||||| |||||   |||||||| |||||  |||||||| | |||||||| |||||||| |||||
----taaataaatgctgtattcttactagacttgttggtggagaactacctaatgcccatgcatgtaacttgcattttactcttttccatgctggcataagcagAAAATTTGGTGGAGAATCTCTTGGGCGATTTTGAGTATGAAGTTCAGATTCCATATTTACTGTATAGAAATGCTGCTCAAGAAGTGAATGGTATCTGGTT

upper sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G08370.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------cttcttcactcttcacactgtgttgttaaactggtacatatggaggaa--aactgatcatt--gtgccag-attcatgaaaagcttaatagtgtcttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT
                                || |   |||  | |  || | | |  | |  || ||    ||     |  | |  |||  ||   || | |||| |     ||  |    |  ||| || ||||||| |||||||| || |  |  | |||||||| |||||| | ||    |||||||| || ||||| ||||| || |||||||||||||| ||||||||
gtcaggatttattcaaataaagttggtgtgtgtcatgtgtctagaaaaggtttagatttagtaatatattgcaagttcttatttaaggattcagtattagtaatcatcagtgtgttgctgtatttgtctggatagATAATCTGGTGGAGAATCTCCTGGGAGATTTTGAGTATGAAGTACAAGGTCCATATTTACTTTACCGTAATGCATCTCAAGAAGTAAATGGCATTTGGTT

upper sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g02870.t01 (Vitis vinifera), 3'ss of exon 3
cttcttcactcttcacactgtgttgttaaactggtacatatggaggaaaactgatcattg-----tgccagattcatgaaaagcttaatagtgtcttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT
        | || |    || ||  ||  | | |||   ||  | | |     |  | ||     || ||  | | |       ||     | ||   | || ||||||| | |||||| || | ||| | |||||||| |||||  |||||   |||||||| ||||||||||||||| |||| ||||| ||||||||||||||
-----atgcgctacttgttgggtatttgcatttgtatccatctatgcatttgtagtaatgggtcttgacatgtcctttttttctttttctttttcccatggaaagATAATCTAGTGGAGAATCTCTTAGGGGATTTTGAGTATGATGTTCAGGTTCCATATTTACTGTACCGAAATGCTGCCCAGGAAGTCAATGGTATTTGGTT

upper sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0080g00860.t01 (Vitis vinifera), 3'ss of exon 3
--cttcttcactcttcacactgtgttgttaaactggtacatatggaggaaaactgatcattgtgccagattcatgaaaagcttaatagtgtcttcttga-cagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT
   |||||    ||| |   | | |||  |   ||  |  |           |  | |||    | |   | | ||   ||   ||  | |     ||| ||||||||||||||||| || | ||| | |||||||| |||||| |||||   |||||| |  | || ||||||||  |||||||||| ||||||||||||||
ttgttcttagtactttat-ttatattgagagggtgtcatttcatctttttcccaaaacataaaacaaatgttaagatgtgcc--atgttattaaaatgagcagATAATTTGGTGGAGAATCTCTTAGGGGATTTTGAGTATGAAGTTCAGGTTCCATATCTATTATATCGAAATGCAGCCCAAGAAGTCAATGGTATTTGGTT

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|93282081|gb|EB674345.1|EB674345
EST:     GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG                         ATAATTTGGTGGAGGATTTATTAAGCCGATTTTGAATATGAACTTTCACCC
genomic: GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGC-GATTTTGAATATGAACTT-CAGCC
EST: gi|78086956|gb|DV515349.1|DV515349
EST:     GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG                         ATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCAC
genomic: GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCAC
EST: gi|148955226|gb|EC900753.2|EC900753
EST:     GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG                         ATAATTTGGTGGAGGATTTATTACGCGATTTTGAATATGAACTTCAGCCAC
genomic: GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCAC
EST: gi|211064273|gb|FK983490.1|FK983490
EST:     GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG                         ATAATTTGGTGGAGGATTTATTAAGCGVTTTTGAATATGAACTTCAGCCAC
genomic: GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCAC
EST: gi|211064272|gb|FK983489.1|FK983489
EST:     GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTG                         ATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCAC
genomic: GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCAC

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: 48 (upstream exon), 48 (downstream exon)
Score: 74

GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GAACTCCCAGCCGAGGTTCCAATTCATTGTCATGAACAGGCGCAACACTGgtacgcacat ... ttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaactgatcattgtgccagattcatgaaaagcttaatagtgtcttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT
                                         tgtcttctt  CT-rich tract
                                  ttaatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttcactcttcacactgtgttgttaaactggtacatatggaggaaaactgatcattgtgccagattcatgaaaagcttaatagtgtcttcttgacagATAATTTGGTGGAGGATTTATTAAGCGATTTTGAATATGAACTTCAGCCACCATATTTGCTGTACCGAAATGCTTCCCAAGAAGTAAATGGTATTTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - cttcaca
- - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - ctggtac
- - - - - - - - - - - - - - - - - - - - - gaggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcatg