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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctgtccgaactgtcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg...

Basic information

species Zea mays
transcript GRMZM2G044137_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044137_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 4
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctgtccgaactgtcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg-
|||||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||| |||||||  ||   ||     ||| | |||   | | |      |  | ||     |  || ||      |||| | |  | |    |  |   ||||||  
ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGgttcgtcgctaccga-----catca-cttacatatatt-----ttcctctatggcaccctcaga--agtactgaatatatttgcctctttccctgtttcag

upper sequence: GRMZM2G044137_T01 (Zea mays), 5'ss of exon 4
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 5'ss of exon 4
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcc----tgttga--attgccattatcttgtttctgtc---------cgaactgtcactgcacaattcttaggccgtcactgcacaattcttaggcc--ctatttgtttcg-----------------------------------------------
|||| ||||| || |||||||||||||||||||||||| | ||  ||   ||    |||| |||||| ||| |||  |    |||||   | | | |  | | |||| ||||          ||||  |     || ||      | || ||    ||    ||   ||| |  |     ||  |                                                
ACAACGTTGACCTGGGCACTGCCTGCGGCAAGTACTACCGCGTCAGCGTGCTGGCCATCACCGACCCCGgtgcgtggcgggatgttggggactacaagcaacatgttgctgttgggcggggacgaagggggcgggcgcatgctacatgctgttggggcttgcttggcagggcagcggcacgtgccacccatcagtgtgctaacggccgctttgttatctggctgaacctgcag
















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|149089950|gb|EE179239.2|EE179239
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60355557|gb|DN222530.1|DN222530
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60394375|gb|DN227245.1|DN227245
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|9824981|gb|BE575183.1|BE575183
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCA
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCA
EST: gi|60338522|gb|DN205495.1|DN205495
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|15100298|gb|BI396089.1|BI396089
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|89251915|gb|DY623701.1|DY623701
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|31406277|gb|CD485009.1|CD485009
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCC
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACT-CGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCC
EST: gi|31441073|gb|CD510504.1|CD510504
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|211067924|gb|FL140850.1|FL140850
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60347030|gb|DN214003.1|DN214003
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|211104174|gb|FL470700.1|FL470700
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|67023955|gb|CO452704.1|CO452704
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60341097|gb|DN208070.1|DN208070
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|27575973|gb|CA998667.1|CA998667
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|76013092|gb|DT940262.1|DT940262
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|211065202|gb|FL140848.1|FL140848
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|211065201|gb|FL140847.1|FL140847
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60357629|gb|DN224602.1|DN224602
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|71299866|gb|DR785955.1|DR785955
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcctgttgaattgccattatcttgtttctgtccgaactgtcactgcacaattcttaggccgtcactgcacaattcttaggccctatttgtttcg

- - - - - - - - - - - - - - - - - - - - - - TGCTGC