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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcag

Basic information

species Zea mays
transcript GRMZM2G702490_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G702490_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g32850.2 (Oryza sativa), 5'ss of exon 4
TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcag
||| || |||||| |||| ||||| || ||||||||   | ||||||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||| ||||| ||    |  ||   ||     ||| | | ||  |||| ||||| ||| || ||  ||| |||  ||||| ||||||||||
TGCCCCGGCTGATATGAAGCAGTCTTTTGACATTCGCCAAGTAATAGCTCGCATAGTTGATGGAAGTGAATTTGATGAATTCAAAAAATTGTATGGAACAgtaagtattttctt----attcttgactaa-gcttgtagtctgtatcttgtgcatcgtgtaagtcgttttctttaactttacatttatgcag

upper sequence: GRMZM2G702490_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G14860.1 (Glycine max), 5'ss of exon 4
TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt---tgttttggacactcagctgtc--atttgcattttgcgtcttatgcattg-tgcaactcaatttgttttcctttaa-atttatgcag-
||| ||  ||||| | || ||    || || ||||| ||| | || |  || |||||||||||||||||||||||||| ||||| ||||||||||| || || |||| ||      |||      | | ||||   |     || |||      |||  ||| |        |  | |||||  |    |  | | ||  
TGCCCCCACTGATCTTAAGCAACAGTTTGATATTCGATCAGTTATTGATCGCATTGTTGATGGAAGTGAATTTGATGAATTCAAGAAATTGTATGGCACTgtgaggacttatccactttacttttttatctgtttaaccattatcttgatatcaatgggttgctatggaatgaccttttttctctcggcacctgtacact

upper sequence: GRMZM2G702490_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G33620.1 (Glycine max), 5'ss of exon 4
TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaagga--ttttgttttggacactcagctgtc--atttgcattttgcgtcttatgcattg-tgcaactcaatttgttttcctttaa-atttatgcag--
||| ||  ||||| | |  ||    || || || || ||| | || |   | |||||||||||||||||||||||||| ||||| ||||||||||| || || ||||  | |    ||      | | ||||   |     || |||      |||  ||| |        || | |||||  |    |  | | ||   
TGCCCCCACTGATCTTAGGCAACAGTTTGATATCCGATCAGTTATTGATAGAATTGTTGATGGAAGTGAATTTGATGAATTCAAGAAATTGTATGGCACTgtgaggacatatccactttactttttatctgtttaaccattatcttgatatccatgggttgctatggaatgatcttttttctctcggcacctgtacactt

upper sequence: GRMZM2G702490_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G34030.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcag
||| ||||  |||   ||||||   || ||  | || || || || ||||| ||||||||||||||||||||||| |||||||| |||   || || || || || ||  |||| |   | || |  |   ||    || || | | || | | || |       || || ||||                 
TGCTCCAGTAGATCACAAACAGCAATTTGATGTGCGGTCTATTATTGCCCGGATTGTTGATGGAAGTGAATTTGACGAGTTCAAGAAACAATACGGCACTgtgag-ataatgttattcgc-cttattttgtatccaaatgttacctttt-tactttcttatgtggaacttctttttggcag-----------

upper sequence: GRMZM2G702490_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0063g00290.t01 (Vitis vinifera), 5'ss of exon 5
TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattttgt----tttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcag
||||||||| ||    || ||||| || ||||| || ||| | || || || |||||||||||||| ||||||||||| ||||| |||||||||||||| || |||   || |    | |  | ||||    |  | |||||| ||   | ||  ||| | |  || |   |    ||    ||   | |||||||
TGCACCAGCAGACCACAAGCAGTCTTTTGACATCCGATCAGTTATTGCTCGCATTGTTGATGGAAGCGAATTTGATGAATTCAAGAAATTGTATGGAACTgtgagggcattttaatatcttaaaactctaa-gctaattgcatgtt--ctttttggcaatttcaaatttggt--aattctagttgtttctatgcag

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|211125174|gb|FL001724.1|FL001724
EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACA                         ACACTAAGTGGACTGGGTTTGCAAGGGATATGTGGGCAACCAGTTGGAA
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTA-GTG-ACTGGTTTTGCAAGG-ATATGTGGGCAACCAGTTGGAA
EST: gi|60341832|gb|DN208805.1|DN208805
EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACA                         ACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCAAGGATATGTGGGCAACCAGTTGGAATTATT
EST: gi|211125176|gb|FL001726.1|FL001726
EST:     GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACA                         ACACTAGTGACTGGTTTTGCA
genomic: GTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattt ... atttatgcagACACTAGTGACTGGTTTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCACCAGCTGATGTGAAACAGTCCTTCGACATTCGTTCAATAATAGCCCGTATTGTTGATGGAAGTGAATTTGATGAGTTCAAAAAATTGTATGGAACAgtaaggattttgttttggacactcagctgtcatttgcattttgcgtcttatgcattgtgcaactcaatttgttttcctttaaatttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG