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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttagccttccacaccaacacttgaagttatccattttgctgttgtctttaatgagaaacattttccattttcctgttgtcttccatcgcactgttgatctcagtcatgacgccagtctctttgacttgcactaccaattataacatctcgtgacttattggactttttgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGTAGGGATCGCACGGAGATGGAAAACGTTATATTCAAGCTTTTTGAAAGGC

Basic information

species Zea mays
transcript GRMZM2G060284_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 4
gtagtttagccttccacaccaacacttgaagttatccattttgctgttgtctttaatgagaaacattttccattttcctgttgtcttccatcgcactgttgatctcagtcatgacgccagtctctttgacttgcactac-------caattataacatctcgtgacttattggactttttgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGTAGGGATCGCACGGAGATGGAAAACGTTATATTCAAGCTTTTTGAAAGGC
                                                                                       ||||    |     ||  || |||||  | | | |||||   |||| |||||       || ||| |   |||| | ||  |||  | ||| ||||   ||||| |||||||||||| |||||   |||||||||||||| |||||||  ||||||||||||| |||  |||||||  |||||||||||||||||||||| |
---------------------------------------------------------------------------------------ccatgttgcca--aatgccaatcatgtggtcggcctcttcatcttgaactactcatcatcagttaaagtttctcataacacatttaattttgtgctcttcagGAGAAGAAGAAGCAAACACCAACCAAACCATCTGATGCAAAAAGAATACGTAGGGATCGCAGGGAACTGGAAAATATTATATTCAAGCTTTTTGAAAGAC
















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|13515926|gb|BG518202.1|BG518202
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|94479553|gb|EB708511.1|EB708511
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|149085564|gb|EE175076.2|EE175076
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTTTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|50324691|gb|CO519817.1|CO519817
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|28187707|gb|CB179317.1|CB179317
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGCGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|94479552|gb|EB708510.1|EB708510
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCCCCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|211224212|gb|FK968311.1|FK968311
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGCGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|149085565|gb|EE175077.2|EE175077
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|13490745|gb|BG517509.1|BG517509
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|76937460|gb|DV175147.1|DV175147
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
EST: gi|211224214|gb|FK968313.1|FK968313
EST:     GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG                         GAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT
genomic: GCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAGgtagtttagc ... tgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttgcactaccaattataacatctcgtgacttattggactttttgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGTAGGGATCGCACGGAGATGGAAAACGTTATATTCAAGCTTTTTGAAAGGC
               ttataac  putative branch site (score: 2)
                                        ctttttgctt  putative PPT
             aattataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttagccttccacaccaacacttgaagttatccattttgctgttgtctttaatgagaaacattttccattttcctgttgtcttccatcgcactgttgatctcagtcatgacgccagtctctttgacttgcactaccaattataacatctcgtgacttattggactttttgcttgccagGAAAAGAAGAAGCAAGCACCAGTGAAACCATCTGATGCCAAAAGAACTCGTAGGGATCGCACGGAGATGGAAAACGTTATATTCAAGCTTTTTGAAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT