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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgggacggagagtgtatgatctaaccgcttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC

Basic information

species Zea mays
transcript AC194970.5_FGT005
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 3'ss of exon 4
cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgggacggagagtgtatgatctaaccgcttacctt-ttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
    |  |||| |   |  |    |  ||  |     |  | |  |  |  || |     |    ||| ||||||  ||| |  | ||||| | |||||||||||||||| ||||||| |||||| |||| || ||||||||||||||||| |||||||||||||| |||||||| || || || ||||||||||||||||
tctgttttaatcattatgcacttctccttgttgctttaatactcctactg-ggaattcttaaaacatgttctaacaacttgctatgttaataactctgcagTTCTTCATATTGCTTTCTTGCTCCTTGGCTGTCTTCTGCAACATGAGCCAGTACCTCTGCATCGGCCGGTTCTCTGCAACTTCGTTCCAGGTCCTGGGCC

upper sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: AT5G42420.2 (Arabidopsis thaliana), 3'ss of exon 3
cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgggacggagagtgtatgatctaaccgcttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
                           | ||| |    |   | |||  |  |   | |  || |||| | | |  |  ||   ||  | || | ||||| | ||||| || || || ||    || || |||||||||||||| ||||| ||||| |||||||||||||| |||||    || ||||| ||  | || |
--------------------------gtaagtatc--tctcttcatggctctgctagtattgt-tatgttatcattggctaatgttcta-caatttgcagCTATTCATTCTTCTCTCATGTGGTCTAGCTGTGTTCTGCAACATAAGCCAGTACCTTTGCATCGGGCGGTTTTCAGCAGTATCGTTCCAAGTTATTGGTC

upper sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: AT1G21070.1 (Arabidopsis thaliana), 3'ss of exon 4
cgaatgataatgaacgtagatgcatatttagtctaaaa----cgaattatgttttgggacggagagtgtatgatctaaccgct--taccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
                        ||  ||  | ||||    | |||   ||||    |     |   | | ||||||    |  || |  | |  ||   | ||||| | ||| || || |||||| |  ||||||| ||||||||||| |||||||| |||||||||||  | ||||| || ||||||||||| || || ||||
-----------------------gtaactatccaaaaatctcctaatcccgtttataaaatcccaac-tcttatctaattattgataaccatcacacaca-tacagTTATGCATTCTTCTCTCCTGCGCATTGGCGGTTTTCTGCAACATAAGCCAATATCTCTGCATCGGAAGATTCTCTGCTACCTCATTCCAAGTTCTTGGCC

upper sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0122g00090.t01 (Vitis vinifera), 3'ss of exon 4
cgaatgataatgaacgtagatgcatatttagtctaaaacgaattat---gttttgggacgga------gagtgtatgatctaaccgcttaccttttaatc----attctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
 | | ||   |     |  |||||||| |  | |  || | ||||    |    |  ||  |      |  |||||      |   ||      ||||||      | ||||||| |||||||| ||||| |||||||| || |||||||||||  ||||||| ||||||||||| || || ||||||||    || ||||||||  | || |
-gtaagaacttatctttctatgcatatattatttctaatggattactgagcacagccacatattatcagtctgtatagatagattcctgctaacttaatccaatggtgtgcagTTTTTCATACTCCTTTCATGCTCCCTAGCAGTGTTCTGCAATGTGAGCCAGTACCTCTGCATAGGACGCTTCTCAGCAGTTTCCTTCCAGGTTTTAGGTC

upper sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: PP1S54_317V6.1 (Physcomitrella patens), 3'ss of exon 5
-cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgg-gacggagagtgtatgatctaaccgcttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
   | |   |   |||  |   |        |    |   || || || ||    |  |   || | |  |   ||    || | | |       | |||||||||| ||||| ||||||||| | || ||||||||||| ||||| ||||||||| | || || || || ||||| ||   | ||||||||          
tttattctcaggaaacagattgggggggggggaggtagtagatttgtgcttaattgttgcttagcgcaaaa--gaataattttcttgtggtattctgtgcagTTCTTTATACTTCTTTCCTGCACACTTGCGGTGTTCTGTAACATAAGCCAATACTTGTGTATTGGACGATTCTCTGCTGTCACATTCCAG----------

upper sequence: AC194970.5_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: PP1S15_387V6.1 (Physcomitrella patens), 3'ss of exon 5
cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgggacggagagtgtatgatc-taaccg---cttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
 |     |  |   |   |  | | || |||  |     ||| |  ||||  |  | |  | ||| |||    || ||   |||   | |       | |||||||||| ||||| ||||| ||  | || ||||||||||||||| ||||||| ||| | |||||||| |||||||| ||     |||| |||          
-gttcattcctttcctggggagaaaatctagcat---gtgaagtgggtttctgctctgctattgtttgactgcaagcggagcttgtttatcgtatcatgtgcagTTCTTTATACTTCTTTCGTGTACACTAGCGGTGTTCTGCAACGTGAGCCAGTACTTGTGCATCGGCCGGTTCTCCGCTGTGACATTTCAG----------

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|211222403|gb|FL093566.1|FL093566
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACT                         TTCTTCATACTGCTTTCCTGCTCCCTGGCCGTGTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAA
EST: gi|149098344|gb|EE184317.2|EE184317
EST:     TCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGGCA-CT                         TTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTTCTGCA-CATGA
genomic: TCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGG-CAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTT-CTGCAACATGA
EST: gi|78087132|gb|DV515525.1|DV515525
EST:     ATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACT                         TTCTTCATACTGCTTTCCTGCTCCCNTGGCG-TGTTCTGCAACATGAGCCA
genomic: ATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCC-TGGCGGTGTTCTGCAACATGAGCCA

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: 192

GCCAATTCAGGCACTTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

GCCAATTCAGGCACTTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 214

GCCAATTCAGGCACTTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

GCCAATTCAGGCACTTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGGCGGTCATTGTTGAACTACCCTTTTTCAGGAGGGGCAACTgtaagttatc ... cattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgggacggagagtgtatgatctaaccgcttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC
                                            tcattct  CT-rich tract
                                      ttttaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgaatgataatgaacgtagatgcatatttagtctaaaacgaattatgttttgggacggagagtgtatgatctaaccgcttaccttttaatcattctgcagTTCTTCATACTGCTTTCCTGCTCCCTGGCGGTGTTCTGCAACATGAGCCAATACCTCTGCATCGGGCGGTTCTCAGCGACCTCATTCCAGGTCCTGGGCC

- - - - - - - - - -atgcata
- - - - - - - - - - - - - - - - - -aaacgaa
- - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg