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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctctccgcactctcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg...

Basic information

species Zea mays
transcript GRMZM2G123969_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123969_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 4
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctctccgcactctcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg-
|||||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||| |||||||  ||   ||     || |  | | | | |  |          ||     |  || ||      |||| | |  | |    |  |   ||||||  
ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgctaccga--catcacttacatatattttcct---------ctatggcaccctcaga--agtactgaatatatttgcctctttccctgtttcag

upper sequence: GRMZM2G123969_T01 (Zea mays), 5'ss of exon 3
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 5'ss of exon 4
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcc----tgttga--attgccattatcttgtttctctccgcactctcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg---------------------------------------------------------------
|||| ||||| || |||||||||||||||||||||||| | ||  ||   ||    |||| |||||| ||| |||  |    |||||   | | | |  | | |||| || |  |           |  |       |||     || ||    | || || | |  |||    |                                                               
ACAACGTTGACCTGGGCACTGCCTGCGGCAAGTACTACCGCGTCAGCGTGCTGGCCATCACCGACCCCGgtgcgtggcgggatgttggggactacaagcaacatgttgctgttggg----cggggacgaagggggcgggcgcatgctacatg-ctgttggggcttgcttggcagggcagcggcacgtgccacccatcagtgtgctaacggccgctttgttatctggctgaacctgcag
















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|211412501|gb|FL461993.1|FL461993
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|113788954|gb|DW908230.1|DW908230
EST:     TCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|33102372|gb|CF062332.1|CF062332
EST:     ACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: ACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|32846856|gb|CD986537.1|CD986537
EST:     ACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGCCACCCAGTGAGCCAGCCCCG
genomic: ACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60357746|gb|DN224719.1|DN224719
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|24769981|gb|CA405110.1|CA405110
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|31355430|gb|CD439787.1|CD439787
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCTGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|32912894|gb|CF017706.1|CF017706
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|15079384|gb|BI388692.1|BI388692
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|32907117|gb|CF011930.1|CF011930
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|67018187|gb|CO446936.1|CO446936
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG

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: 1105

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 803

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 730

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 596

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctctccgcactctcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg

- - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctccgc