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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataatgtgttttgtttaat...

Basic information

species Glycine max
transcript GLYMA02G42560.1
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 12
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataat-gtgttttgtttaat---------------------------
 || ||||| || ||| | ||||| ||   ||||||||||  ||||||||||||||| ||||||||  | ||||| ||||| || ||||||||||| |||||  |   |||     ||    |  ||| |   | ||  | | | | || ||  ||  ||    | |||    |     | ||  | |  || || ||| |                           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTATCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgt--ttggttcgaaccca----ttgtat-tggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacgcatccaatcatatgtaatgcag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgat--taggtttaccattattcttggataatgtgttttgtttaat---------------------------
 || ||||| || ||| | ||||| ||   ||||||||||  ||||||||||||||| ||||||||  | ||||| ||||| || ||||||||||| |||||  |   |||     ||    |  ||| |   | ||  | | | | || ||  ||  ||  ||  |  | ||  |  |||      ||  || || ||| |                           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgt--ttggttcgaaccca----ttgtat-tggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgct-tgcattctgattagtaaacacatccaatcatatgtaatgtag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 11
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataat-gtgttttgtttaat---------------------------
 || ||||| || ||| | ||||| ||   ||||||||||  ||||||||||||||| ||||||||  | ||||| ||||| || |||||||||||  ||||  |   |||     ||    |  ||| |   | ||  | | | | || ||  ||  ||    | |||    |     | ||  | |  || || ||| |                           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGAAGgt--ttggttcgaaccca----ttgtat-tggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacgcatccaatcatatgtaatgcag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 4
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgc----taaattcagtttcaaacttcatat---ataattcattttcttgcaatatcttgtttg--attaggtt-taccattattcttggataatgtgttttgtttaat-------------------------
 |||||||| |||||| | ||||| |||   |||||||||  |||||||||||| || ||||||||  | ||||| |||||||| |||||||| || |||||       |||  || |  |     | ||||      | |  |  |     |||    | |  |   | ||||  ||   |   |  | |  |  |  || || |||                           
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 7
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataat-gtgttttgtttaat---------------------------
 || ||||| || ||| | ||||| ||   ||||||||||  ||||||||||||||| ||||||||  | ||||| ||||| || ||||||||| | |||||  |   |||     ||    |  ||| |   | ||  | | | | || ||  ||  ||    | |||    |     | ||  | |  || || ||| |                           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTAAGCAGgt--ttggttcgaaccca----ttgtat-tggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacacatccaatcatatgtaatgcag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 12
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgt---gctaaattcagtttca--aacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataatgtgttttgtttaat
 || ||||| || ||| | ||||| ||   ||||||||||  ||||||||||||||| ||||||||  | ||||| || || || ||||||||||| |||||   | |  |  |  ||  |    ||    ||||   ||    | | |  |      | |    | ||   || | |    |        |||           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTTCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgtgtcggcgtttcgagaccgaggggtcc-ctgggccgacgagtgaaatgtcgctgcgtgccccagc----

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgt---gctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtt-taccattattcttggataatgtgttttgtttaat-------------------------
 |||||||| |||||| | ||||| |||   |||||||||  |||||||||||| || ||||||||  | ||||| |||||||| ||||| || || |||||   | | ||  |  ||  |   || |   |||||       || || |||   |  || || ||||  ||   |   |  | |  | ||  || || |||                           
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattcta---ttgactgataatatgaga-ctagcgataagctaattcataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 27
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataat-gtgtttt-gtttaat
||| ||||| || ||||| |||||||| || |||||||| ||||| |||||||| || ||||||||||| ||||||||||||||||||||||||||  |||| |  |      |     | |    | | |  || ||  ||      ||  | ||  |  |  | ||  || | ||    |   |  ||   | |  ||| 
GTCGAAGAAAGACAACCTGTACAAAGACGCGATGGAGACTGCCTCGCAATCTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgtacccagaatgctagagcaatctgaagacatctctttaactaaagccatagtcttccacaa--tataaaatcaatcacacaccttcatgcactagcataac

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 27
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataatgtgttttgtttaat--
 || |||||||||||| | ||||| ||||||||||| || ||||||||||| ||||| ||||| ||||||||||| ||||||   |  ||  | ||  ||||    |||| | ||      |   ||| |   | |   |  |||| |||     |  ||||   ||     || |  ||  || || | | | |   |   
TTCTAAGAAGGATAACTTGTACAAGGATGCCATGGAAACCGCCTCACAATCAGGCGATCGTGATCTTGCTGAGGAATTGCTTACCTTCTTTGTGGACAAGgtagctaattgatttatgttatcattatttggctaaggcttatgca-tattaaaataaattaa--ttgattctaattctgcgtattgggatgtatgacacag

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|7327210|gb|AW620932.1|AW620932
EST:     CCGGGGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAG                         GGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATCTCATA
genomic: CTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaatt ... gcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATA
EST: gi|16106177|gb|BI893917.1|BI893917
EST:     CTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAN                         GGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATCTGATA
genomic: CTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaatt ... gcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATA
EST: gi|192334749|gb|FK025254.1|FK025254
EST:     GGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAG                         GGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATC
genomic: GGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaatt ... gcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgattaggtttaccattattcttggataatgtgttttgtttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG