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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttttcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag

Basic information

species Zea mays
transcript GRMZM2G141587_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 15
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttttcatcac-ttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag
|||||||||||| |||||  |||| ||||| |||||||||||||||||||| |||||||| |||||||| |  || |||||||||||||||||||||||||| ||| ||||||| |  | |||||  ||| | | ||||  ||   ||||||   || ||    ||||        |   ||||| |||  || | ||   |        
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTCACGACTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatgcattc-acatatgatttg-gttagactgttaattttcagag-------gtagtataactattcgatgtattacag--------

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttttcatcac-ttaaaaagacatcct-atatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag
|||||||||||| |||||  |||| ||||| ||||||||||| |||||||| |||||||| |||||||| |  || |||||||||||||||||||||||||| ||| ||||||| |  | ||||| ||||  | | ||||  ||   |||||| | || ||    || |        |   ||||| |||  || | ||   |        
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgatgtattacag--------

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 19
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttttcatca----cttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag
  |||| | ||| |||||||| ||||||||  |||||||||| |||||||| ||||| |  || ||||| ||| | |||||||||||||| || || ||||| ||  |  |    |     ||  ||||| |   | ||| | ||| |  ||     | ||   |||  ||| ||    |   || ||                         
CAATGAAACCAATGAACGTGTTCGGACTGGCTTATGGGTTGGGGATTGTTTTATCTATACCAACTCTTCTTGGAGGCTTAATTACTGTGTTGGTGGTGAGgtaaggctcatttctaggtttttggaaagaaacgttttatgttttttattttgttgtaattg-agattcagtactcctcttatattacag-----------------------

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 15
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgt---gagttttttcatcacttaaaaagacatcctatatatcttt-caagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag
 |||||||  || ||| | ||  | |||||  |||||||||| || |||||||| ||||| || || || ||||| |||||||||||||| || || |||||   | || || ||  | |||     || |   | |  || | | ||  | | |||  ||    || ||    |||| ||         | | | ||   ||| |||| |||
CCATGAGACAAATGAAAGAGTTAGAACTGGTATATGGGTTGGAGACTGTTTCATTTACAACAACTCCTCTTGGCGGCTTAATTACTGTGTTGGTGGCGAGgtattgtgtattgtccacccttgtcttgaaagtatttccatatgtgcagatgatatccatttc--atgga----tttcttggagcttttttgttaaataaccatatgttccag

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
lower sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt---tcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag
 ||||||||   ||| || ||  | |||||  ||||||| |||||||||||||| ||||| || || |||||| | || || ||||| || |||||||||||  | ||||   |  ||  ||| |      ||  |  |    ||| ||                                                               
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttttgtattgtcgtttatatttgtttcacacttcctcttccag---------------------------------------------------------------

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
lower sequence: EFJ09529 (Selaginella moellendorffii), 5'ss of exon 10
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt---tcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag
 ||||||||   ||| || ||  | |||||  ||||||| |||||||||||||| ||||| || || |||||| | || || ||||| || |||||||||||  | || |   |  ||  ||| |      ||  | ||    ||| ||                                                               
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttctgtgttgtcgtttatatttgtttcacacatcctcttccag---------------------------------------------------------------

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|18384334|gb|BM417533.1|BM417533
EST:     TCATCTACAATAATTCTTCATGGTGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|18384433|gb|BM417632.1|BM417632
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|22489660|gb|BU049570.1|BU049570
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|21809537|gb|BQ667855.1|BQ667855
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTG-GTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|18649807|gb|BM498626.1|BM498626
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|18649903|gb|BM498722.1|BM498722
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|89106141|gb|DY576358.1|DY576358
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|211344820|gb|FK991758.1|FK991758
EST:     CATCTACAATAATTCTTCATGGCGGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: CATCTACAATAATTCTTCATGGCG-TCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|211344819|gb|FK991757.1|FK991757
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT
EST: gi|18963894|gb|BM660690.1|BM660690
EST:     TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAG                         GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCNT
genomic: TCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttt ... tgtgttacagGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttttcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA