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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcagaatcttcagacctggccagctgaatactgttttaccataccgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA

Basic information

species Zea mays
transcript GRMZM2G073535_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073535_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g41900.3 (Oryza sativa), 3'ss of exon 3
gtattcagaatcttcagacctggccagctgaatactgttttacca-taccgatagat-gttcaatctgttaatactgatcgtgcaattattacttgtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA-------------------------------------------------------
||||| |||||  ||||| | |  |       |        |  | | | | ||  | |  | || | |  || ||||   ||   || |  ||  | ||| |||||||||||||| ||||| || ||||||||||||||||| ||||||                                                       
gtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttat--attctgaatctgattttttatctctttttgctagGCTGGGATTGCTAAGAAGGACAACATCAAGATTCACGGTTTCTAAGCTGCCTATAGATGCTCGTATGCAATATCGTGTGCTGCCAGATATTGGGAAGCCT
















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|211042766|gb|FL410377.1|FL410377
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32915153|gb|CF019965.1|CF019965
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32915467|gb|CF020279.1|CF020279
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|166488253|gb|EG202729.1|EG202729
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCG
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCG
EST: gi|211254796|gb|FL420511.1|FL420511
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211199110|gb|FL383374.1|FL383374
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|76921765|gb|DV168690.1|DV168690
EST:     GACCCAGAGCTAGGCCAG
genomic: TCAGCTCCAAGGTGACCA
EST: gi|28188096|gb|CB179706.1|CB179706
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211433580|gb|FL370258.1|FL370258
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211275053|gb|FL384325.1|FL384325
EST:     GACCCAGAGCTAGGCCAG
genomic: TCAGCTCCAAGGTGACCA
EST: gi|211334569|gb|FL404956.1|FL404956
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|91874020|gb|EB403977.1|EB403977
EST:     GGACCCAAAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211497349|gb|FL428240.1|FL428240
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32915137|gb|CF019949.1|CF019949
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211360773|gb|FL397053.1|FL397053
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|28930990|gb|CB334351.1|CB334351
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|13315834|gb|BG410386.1|BG410386
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCGCGGGTTCTAA
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA
EST: gi|32915018|gb|CF019830.1|CF019830
EST:     GGACCCGGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32864981|gb|CF004663.1|CF004663
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211006247|gb|FL408517.1|FL408517
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211490127|gb|FL369784.1|FL369784
EST:     GTCATTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG          
genomic: GTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagG
EST: gi|14244595|gb|BG842533.2|BG842533
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32937269|gb|CF042088.1|CF042088
EST:     GGACCCAGAGTTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211108516|gb|FL304066.1|FL304066
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32864386|gb|CF004068.1|CF004068
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211207669|gb|FL419154.1|FL419154
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211042145|gb|FL385023.1|FL385023
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|6021595|gb|AW066523.1|AW066523
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|32865535|gb|CF005217.1|CF005217
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|13490598|gb|BG517362.1|BG517362
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA
EST: gi|6012307|gb|AW061663.1|AW061663
EST:     GGACCCACAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211332492|gb|FL407989.1|FL407989
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA
EST: gi|211134617|gb|FL369499.1|FL369499
EST:     GGACCCAGAGCTAGGCCAG
genomic: TTCAGCTCCAAGGTGACCA

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: 703

GTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1226

GTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1982

GTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1026

GTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA
                      tactgat  putative branch site (score: 1026)
                                          cttgtctt  putative PPT
                                  aattattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcagaatcttcagacctggccagctgaatactgttttaccataccgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA