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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacacgtaatttttttttcttcctcctccctacactacacagcagtgtttctgaacggaacaggactgaccgtcgtttcagGACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCACGACGTATGATCTGGATGGAGATTTCAAG

Basic information

species Zea mays
transcript GRMZM2G454928_T06
intron # 5
splice site 3'
intron type U2

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|71320939|gb|DR797186.1|DR797186
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAG                         GACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCAC
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGgcacacgtaa ... gtcgtttcagGACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCAC
EST: gi|71320936|gb|DR797185.1|DR797185
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAG                         GACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCAC
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGgcacacgtaa ... gtcgtttcagGACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCAC
EST: gi|110521286|gb|EE025470.1|EE025470
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|110521286|gb|EE025470.1|EE025470
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|110521286|gb|EE025470.1|EE025470
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|110521286|gb|EE025470.1|EE025470
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|110521286|gb|EE025470.1|EE025470
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|110521286|gb|EE025470.1|EE025470
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78109734|gb|DV528150.1|DV528150
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78109734|gb|DV528150.1|DV528150
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78109734|gb|DV528150.1|DV528150
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78109734|gb|DV528150.1|DV528150
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78109734|gb|DV528150.1|DV528150
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78109734|gb|DV528150.1|DV528150
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78022296|gb|DV490683.1|DV490683
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78022296|gb|DV490683.1|DV490683
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78022296|gb|DV490683.1|DV490683
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78022296|gb|DV490683.1|DV490683
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78022296|gb|DV490683.1|DV490683
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-
EST: gi|78022296|gb|DV490683.1|DV490683
EST:     AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAAGG                         C
genomic: AGTTCGTCAAGGCGACATGGAAACTAAGGTTCATCTTCAAGCTCCAAAA-Ggcacacgtaa ... gtcgtttcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctacactacacagcagtgtttctgaacggaacaggactgaccgtcgtttcagGACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCACGACGTATGATCTGGATGGAGATTTCAAG
                                     gactgac  putative branch site (score: 2)
                                              tcgtttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacacgtaatttttttttcttcctcctccctacactacacagcagtgtttctgaacggaacaggactgaccgtcgtttcagGACGTATCTGAGGCTTCCATGGAGGCCGCTGGTCGCGATCGGAGGGAGCACGACGTATGATCTGGATGGAGATTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT