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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACTTCGACCTGAGCGGCACGGCGTTCGGAGCCATGGCGAAGGACGGCCAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagctagcagcgccgccgcgcccgtaccgcgcgcgcgcgctcagatgcttctaagcagcaggactgtcgtactacggtacgactacctgtgttt...

Basic information

species Zea mays
transcript GRMZM2G026956_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026956_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g44106.1 (Oryza sativa), 5'ss of exon 3
TGCACTTCGACCTGAGCGGCACGGCGTTCGGAGCCATGGCGAAGGACGGCCAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagctagcagcgccgccgcgcccgtaccgcgcgcgcgcgctcagatgcttctaagca-gcaggactgtcgtactacggtacgactacctgtgttt
| ||||||||||||||||| ||||||||||| |||||||| ||   ||||||||  || |||||||||  ||||||  | |||    |||| ||| || ||||| | || || |     |    |  | |||   | |   |  | |||     | | |   |      || |   ||    |  ||          ||  
TCCACTTCGACCTGAGCGGGACGGCGTTCGGCGCCATGGCAAAACCCGGCCAGGACGATCAGCTCCGCAACGCCGGCAAGCTCCCAGTCCAATACGCTAGgtaatcaagatatctatctctatccatctgtatatctctatctagatcaatcaatcccatatatatcctacagctatagctagcaacagtcgatcaagtg-
















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|50327792|gb|CO522918.1|CO522918
EST:     CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCG                         GGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
genomic: CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagc ... gtgcgtgcagGGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
EST: gi|71768749|gb|DR966686.1|DR966686
EST:     CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCG                         GGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
genomic: CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagc ... gtgcgtgcagGGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
EST: gi|74242240|gb|DT650154.1|DT650154
EST:     CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCG                         GGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
genomic: CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagc ... gtgcgtgcagGGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
EST: gi|4885999|gb|AI677119.1|AI677119
EST:     CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCG                         GGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
genomic: CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagc ... gtgcgtgcagGGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
EST: gi|50334672|gb|CO529798.1|CO529798
EST:     CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCG                         GGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG
genomic: CAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagc ... gtgcgtgcagGGTGCCGTGCAACTGGCGAGGGCTGGACATCGCGTTCAAGGTGGACGCCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCACTTCGACCTGAGCGGCACGGCGTTCGGAGCCATGGCGAAGGACGGCCAGGCGGACCAGCTCCGCGGCGCCGGACACCTCAAGATCCAGTACACTCGgtaagctagctagcagcgccgccgcgcccgtaccgcgcgcgcgcgctcagatgcttctaagcagcaggactgtcgtactacggtacgactacctgtgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC