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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaatcttgagaaacatttgatggtagtatgggttcatttgtcatgcatacatgtgacacttttttattctccatatttatttcatttggcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCAGTCGAGCCAGCAAGAATGGCAGTAGCAGCTGGCCTATCAGATGGGTTGT

Basic information

species Zea mays
transcript GRMZM2G006468_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006468_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 7
tgtaatcttgagaaacatttgatggtagtatgggttcatttgtcatgcatacatgtgacacttttttattctccatatttatttcat-----ttggcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCAGTCGAGCCAGCAAGAATGGCAGTAGCAGCTGGCCTATCAGATGGGTTGT
   ||| | ||  |    ||| || |   |||  || |      ||  ||  ||| || ||   |    | || ||  |||   |||     ||| ||||||||||||||| |||||||||||||||| |||||||||||||| ||||| ||| ||||||||||||||||||||||  ||||||| ||| | || || |||||||
--gaatttagaccagttcttgctgctcacatgatttaaccga--atctatctatg-gaaacaaataatgtatctatgcttacaccattggccttgacatgaacagGTTCCTATACAAGTCCATAGAAGCCTTGCATACAGTGATGGCATAAGATCAGTCGAGCCAGCAAGAATGGCGATAGCAGCCGGCATGTCTGACGGGTTGT
















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|60355084|gb|DN222057.1|DN222057
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|5895762|gb|AW037008.1|AW037008
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTT
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTT
EST: gi|74242180|gb|DT650094.1|DT650094
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|13178078|gb|BG349336.1|BG349336
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
EST: gi|31250432|gb|CD219456.1|CD219456
EST:     CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAG                         GTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA
genomic: CCTTCGATCTTCGGCCTTCAGATGCCATAAACATTGCTGTTCGTTGCAAGgtatttgctg ... gcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatacatgtgacacttttttattctccatatttatttcatttggcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCAGTCGAGCCAGCAAGAATGGCAGTAGCAGCTGGCCTATCAGATGGGTTGT
                ttttttattctccata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaatcttgagaaacatttgatggtagtatgggttcatttgtcatgcatacatgtgacacttttttattctccatatttatttcatttggcatgaacagGTTCCTGTACAAGTCCATAGAAGTCTTGCATACAGTGACGGCATCAGACCAGTCGAGCCAGCAAGAATGGCAGTAGCAGCTGGCCTATCAGATGGGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG