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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcatctttgttactaaattccacttgtagtttttgtacacaagttctgtggctaatgtaccttattattgcag

Basic information

species Zea mays
transcript GRMZM2G141587_T02
intron # 16
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 16
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 7
GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttca---tctttgttactaaattccact-tgtagtttttgtacacaagttctgtggctaatgtaccttattattgcag
|||||||| || |||||||||||||||| |||||||||| | ||||||||||| |||||||||||||||||||||||||| |||||||||||||||||      | | || || |  ||   | | || ||      |  ||   ||||| || |||  |   || ||| |||||
GTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAAgtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaac---ttctgaggttaacttgttttcttactgcag

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 16
GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttca---tctttgttactaaattccacttgtagtttttgtacacaagttctgtggctaatgtaccttattattgcag
|||||||| || |||||||||||||||| |||||||||| | ||||||||||| ||||||||||||||||| |||||||| |||||||||||||||||      | | || ||    ||   | | | |        |   || ||||| || |||  |   || ||| |||||
GTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTACCTTATTGACAAGCAATTTAAgtgagtcttggttgtctggtatcgtatcatattcggaagcc--acaatgaacttctgaggttaacttgttttcttactgcag

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 16
GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcatctttgttactaaattccacttgtagtttttgtacacaagttctgtggctaatgtacc--ttatta-ttgcag-------
|| || ||  ||||||| ||||| || || ||||| || || |||||||||||||||||||| ||||| ||| | ||||| ||  | ||||||| |||  | |||  |   |  |||  | |   ||||||      |||      || ||| | | |   |||| | |||          
GTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAAgtaagtgaaacttc-tgcttggatt--attcaaagttttaaattgcaataatcttgactatttttctgtttatcaattgtttttctcag

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 16
GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcatcttt-------gttactaaa---ttccacttgtagtttttgtacacaagttctgtggctaatgtaccttattattgcag
|| || ||  ||||||| ||||| || || ||||| || || |||||||||||||||||||| ||||| ||| | ||||| ||  | ||||||| |||  | |||         ||| | ||   ||  | ||| |||  |  |  || | || | ||  ||    |  || || |  |||
GTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAAgtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttg-actacttttctgtttatc--aattttttttctcag

upper sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 16
GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcatctttgttactaaattcca-----cttgtagtttttgtacacaagttctgt---ggctaatgtaccttattat-tgcag
|| || ||  ||||||||||||| ||||| |||||||| |||||||||||||| |  ||||| || || |||||||| || ||  | ||||||||||   | ||| |   ||  | | |      ||    | |||||| |      |   |      | || ||  ||||  | |||||
GTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAAgtgaggg-agcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcag

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:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGTGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|18384433|gb|BM417632.1|BM417632
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCCATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|211291668|gb|FL235608.1|FL235608
EST:     TTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAGACACTTGT
genomic: TTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|22489660|gb|BU049570.1|BU049570
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|21809537|gb|BQ667855.1|BQ667855
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|18649807|gb|BM498626.1|BM498626
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|18649903|gb|BM498722.1|BM498722
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|89106141|gb|DY576358.1|DY576358
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
EST: gi|18963894|gb|BM660690.1|BM660690
EST:     GGATATCNTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCCATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcat ... attattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttcatctttgttactaaattccacttgtagtttttgtacacaagttctgtggctaatgtaccttattattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA