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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttttttaactgttggcgatcttattatttgtatttttcttttttgtgtcagtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA

Basic information

species Zea mays
transcript GRMZM2G402002_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18
gtgagtcttttttaactgt-tggcgatcttattatttgtatttttcttttttgtgtca-gtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
                 || ||    | | ||| |||  | |      | |  ||  |  | ||||| |         ||| |    | || |   | |||| |||||| |||||||| ||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| ||  ||||  |||| || ||||
-----------------gtatgattgtttaattgtttacagtgcaacgtatgatgctatattcctaacttccac---agctaac-attttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgagtctttttt-------aactgttgg-cgatcttattatttgtatttttct--tttttg--tgtca-gtccctaattgttggttgggctgatt-gctattgtgtattt-ttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
|| |  | ||||        || ||||   |  ||||  |||   ||  |  |   | || |  ||| | || |  ||    |    || ||  || | |  | ||| ||| ||    |||| |||||| | ||||| || ||| | ||| |||| || ||||||||||||||||| ||||||||||| ||  |||||||  ||||| | ||  | || |
gtaaaacgttttggatacgaaattgtttttccgtctttatatgaatacatgccaaatcttagattgttatgttcacaagaactcaccggactcttttgattatctgtgtttgttttaaagCACGAGGAAGGTGCGATCGAGGAGAGAGCTCGGGACTATAATGCAAACTGGATGACGGCAGTTGAGATACTCAATGATGACATCTACCTCGGTACTGATA

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgagtcttttttaactgttggcgatcttattatttgtatttttcttttttgtgtcagtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
    || |   ||  ||    |  || |   | |||  |   |  | |  | |||   |     ||||||  |  |   | ||  | |||  | |        |||| |||||| | || ||||| ||||| ||| |||||||||||||||| |||||| | || |||||||| || ||||||||  | ||| | || || ||||
----gtataactt--ctagacgaaatttgtgtgtttaaaaactgatctactatgttcatttggtattgtt--tctgatggcttattcttgaatgt-----aaaagCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 18
--------------------gtgagtcttt-----tttaactgt-----tggcgatctt----attatttgtatttttcttttttgtgtcagtcc---ctaattgttggttg--ggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
                    || |  | ||     |||  | |      ||||| ||       |||   |  | ||   ||| | ||| | ||    |   |||||  | |  | ||||||| |  | | | | |||   |||||||||||| | || ||||||||||| ||  | || ||||||||||| |||||| | || |||||||| |||||||||||  | ||| |||| || ||||
gtaagatgactaatcttcaagtaatcccttgtccttttggcagcaagtatggcgttccctggagttaaaagagtgttgtgtttgtttgttactcttatcgtcttgttaatggatgtctgattggtcctttttttatttt--cagCATGAGGAAGGTGCCATTGAAGAGCGAGCCCGTGACTACAATGCAAATTGGATGTCAGCTGTTGAGATTCTTGATGATGACATTTACCTTGGTGCTGAGA

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ23079 (Selaginella moellendorffii), 3'ss of exon 18
gtgagtcttttttaactgttggcgatcttattatttgtatttttcttttttgtgtc-agtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
                                         | |  | |||||    |||   |  ||| |  | || ||| || ||| |             ||||  |||||| | ||||| ||||| || ||  |||||||||| ||||||||||||||||| || ||||| || || || ||  ||||| | || || ||||
----------------------------------------gtatgctctttgtacagagtgttttcttgcttat-ggactgtttactacttca----------cagCCGGAGGAAGGAGCGATCGAAGAACGCGCGCGGGATTACAACGCAAACTGGATGACTGCTGTGGAGATCCTGGACGACGACATCTACCTCGGAGCCGAGA

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 18
lower sequence: EFJ30457 (Selaginella moellendorffii), 3'ss of exon 18
gtgagtcttttttaactgttggcgatcttattatttgtatttttcttttttgtgtcagtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
                                        | | || ||    |  |||   |  ||| |  | |  ||| || ||| |             ||||  |||||| | ||||| ||||| || ||  |||||||||| ||||||||||||||||| || ||||| || || || ||  ||||| | || || ||||
---------------------------------------gtatgctcttcgtagagagtgttttcttgcttat-gaactgtttactacttca----------cagCCGGAGGAAGGAGCGATCGAAGAACGCGCGCGGGATTACAACGCAAACTGGATGACTGCTGTGGAGATCCTGGACGACGACATCTACCTCGGAGCCGAGA

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|7031241|gb|AW461129.1|AW461129
EST:     TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACT-G
EST: gi|32943908|gb|CF048727.1|CF048727
EST:     TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
EST: gi|211183656|gb|FL219824.1|FL219824
EST:     TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
EST: gi|6973667|gb|AW438241.1|AW438241
EST:     TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGG

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 6 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 346

TGGCCACCATGGGCACATACTTGCCTTGTATACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 4

TGGCCACCATGGGCACATACTTGCCTTGTATACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 165

TGGCCACCATGGGCACATACTTGCCTTGTATACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 6

TGGCCACCATGGGCACATACTTGCCTTGTATACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 95

TGGCCACCATGGGCACATACTTGCCTTGTATACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 212

TGGCCACCATGGGCACATACTTGCCTTGTATACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAATCAATATCCTTGCTGGTGTATAAGgtgagtcttt ... ttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcagtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA
                                          tattttt  CT-rich tract
                                   tattgtgtattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttttttaactgttggcgatcttattatttgtatttttcttttttgtgtcagtccctaattgttggttgggctgattgctattgtgtatttttgggcagCATGAGGAAAGCGCGATTGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTACGTTGGGGCGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG