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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagccttgaactatttttttcgaaaggaagccttgaactattttaagacagtaccatgaaacctgtgttaggatccctactgattgccctttttttttcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG

Basic information

species Zea mays
transcript GRMZM2G165747_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 13
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 11
gtattagccttgaactatttttttcgaaaggaagccttgaactattttaagacagtaccatgaaacctgtgttaggatccctactgattgcc-ctttttttttcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                                               ||| |     | | ||    |    |||  ||   | |||      | || |||    |  | |||||||||||||||||||||||||| |||||||||||||||||    ||||||||||||||||||| ||||||||||| ||||| ||||| || || || |
----------------------------------------------gtaaaa-gacgcgacgag--tttctatagcttcgtgaatgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

upper sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 13
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
gtattagccttgaactatttttttcgaaaggaagccttgaactattttaagacagtaccatgaaacctgtgttaggatccctactgattgcc-ctttttttttcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                                               ||| |     | | ||    |    |||  ||   |||||      | || |||    |  | |||||||||||||||||||||||||| |||| ||||||||||||    ||||||||||||||||||| ||||||||||| ||||| ||||| || || || |
----------------------------------------------gtaaaa-gacgcgacgag--tttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
















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|78024981|gb|DV493368.1|DV493368
EST:     TGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: TGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211313753|gb|FL309496.1|FL309496
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|32862876|gb|CF002558.1|CF002558
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211327188|gb|FL127497.1|FL127497
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|60353479|gb|DN220452.1|DN220452
EST:     TGTCCACTCTTTCAGAAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: TGTCCACTCTTTCAG-AATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|60344097|gb|DN211070.1|DN211070
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|32850521|gb|CD990202.1|CD990202
EST:     CTGTCCACTCTTTCAGAATCACCACCTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGCCATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|31362393|gb|CD446750.1|CD446750
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|33091691|gb|CF051685.1|CF051685
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|67026378|gb|CO455127.1|CO455127
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|33100623|gb|CF060583.1|CF060583
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211093163|gb|FL309351.1|FL309351
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|29130048|gb|CB380752.1|CB380752
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|32849879|gb|CD989560.1|CD989560
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|31362419|gb|CD446776.1|CD446776
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|24769384|gb|CA404513.1|CA404513
EST:     TGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCAT
genomic: TGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCA-CCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCAT
EST: gi|32944358|gb|CF049177.1|CF049177
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|32847292|gb|CD986973.1|CD986973
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211331517|gb|FL127526.1|FL127526
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211329357|gb|FL127510.1|FL127510
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211468384|gb|FL469331.1|FL469331
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGG                         ATCCACACCCATATGTG-NACTCCAACTTCAACGACATCATCCACTCCAT
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCA-Ggtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCAT
EST: gi|211335855|gb|FL127558.1|FL127558
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211333680|gb|FL127538.1|FL127538
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|211329356|gb|FL127509.1|FL127509
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAAACTTCA-CGACATCATCCACTCCAT
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAA-CTTCAACGACATCATCCACTCCAT
EST: gi|32944605|gb|CF049424.1|CF049424
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|32923062|gb|CF027874.1|CF027874
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|32929227|gb|CF034039.1|CF034039
EST:     CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
EST: gi|213172844|gb|FM183801.1|FM183801
EST:     CTGTCCACTCTTTNNNAATCACCAACTGCGGAGTCCAGGACACCACCCAG                         ATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC
genomic: CTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATC

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), 26 (downstream exon)
Score: 9

GGAGGGTCTGCCACTGCGCAAGTCAGAGCATGCATTCTACCTGGACTGGGCTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG


Block sizes: 49 (upstream exon), 26 (downstream exon)
Score: 4

GGAGGGTCTGCCACTGCGCAAGTCAGAGCATGCATTCTACCTGGACTGGGCTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 18

GGAGGGTCTGCCACTGCGCAAGTCAGAGCATGCATTCTACCTGGACTGGGCTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 59

GGAGGGTCTGCCACTGCGCAAGTCAGAGCATGCATTCTACCTGGACTGGGCTGTCCACTCTTTCAGAATCACCAACTGCGGAGTCCAGGACACCACCCAGgtattagcct ... tcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatgaaacctgtgttaggatccctactgattgccctttttttttcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                         tactgat  putative branch site (score: 59)
                     tccctactgattgccc  CT-rich tract
                                     tttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagccttgaactatttttttcgaaaggaagccttgaactattttaagacagtaccatgaaacctgtgttaggatccctactgattgccctttttttttcttggatagATCCACACCCATATGTGCTACTCCAACTTCAACGACATCATCCACTCCATCATCGACATGGACGCAGATGTGATCACCATCGAGAACTCCCGGTCCGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG