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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGAGTGCATCGAGGTTCATTAAGTGCGTCACCGTCGGCGACGGCGCTGTCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttctttctcctcttcccaattataactatctgtagttaaaattagatatatatgcgtttgaattgtaaaactcctataatttggagtttccaac...

Basic information

species Glycine max
transcript GLYMA06G02580.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 1
AATGAGTGCATCGAGGTTCATTAAGTGCGTCACCGTCGGCGACGGCGCTGTCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttct-ttctttctcctcttcccaattataactatctgtagttaaaattagatatatatgcgtttgaattgtaaaactcctataatttggagtttccaac
 ||||| || || |||||||| ||||||||||||||||| |||||||| |||||||| |||||| || | || |||||||||  |||||| || ||||| ||   | |||||  || |||||    |  |     ||   |  |    ||   |   | | | | |   || |    || || |  ||     |||   | 
GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACCGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACTgtgcgtattcttcttcttcttcttcttcttcttcctccaaacatttccttttcttcttcttcttctttcttttgcttcttctttttttaattatttttga-

upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM5G803949_T01 (Zea mays), 5'ss of exon 1
AATGAGTGCATCGAGGTTCATTAAGTGCGTCACCGTCGGCGACGGCGCTGTCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttctttctcctcttcccaattataactatctgta-gttaaaattagatatatatgcgtttgaattgtaaaactcctataatttggagtttccaac
 ||||| || || |||||||| ||||||||||| ||||| |||||||| |||||||| |||||| || | ||||||||||||  |||||| || ||||| ||  |   | | |||||||  |   ||  |  | | | |  |     | |      || |    |||    |     ||      || ||| |    |   
GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACGGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATTTCCTACACCTCCAACACCTTCCCCACCgta-cgcccctcctcctctgacggtttcaatttttttttctggggggagtccccggattttgaattgcggcggcggtcttgatcgatctggggcgcgctgg

upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 1
AATGAGTGCATCGAGGTTCATTAAGTGCGTCACCGTCGGCGACGGCGCTGTCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttctttctcctcttcccaattataactatctgtagttaaaattagatatatatgcgtttgaattgtaaaactcctataatt-tggagtttccaac--
 ||||| || || |||||||| ||||||||||| ||||| |||||||| |||||||| |||||| || | || |||||||||  |||||| || ||||| ||    | ||| |||||| |     ||    |  |    || |   |||   | |    | ||     |     |  |   ||      || |||    |   
GATGAGCGCGTCCAGGTTCATAAAGTGCGTCACGGTCGGGGACGGCGCCGTCGGCAAGACCTGCATGCTCATCTCCTACACCTCCAACACCTTCCCCACCgtacgctccttcctcctcatt---gttgctccgctggagaggtttcatttttttttggggggtcccggtccgggattttgaattgcgacggcgttcttgatcg

upper sequence: GLYMA06G02580.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 1
AATGAGTGCATCGAGGTTCATTAAGTGCGTCACCGTCGGCGACGGCGCTGTCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttctt-tctcctcttcccaattataactatctgtagttaaaattagatatatatgcgtttgaattgtaaaactcctataatttggagtttccaac-----
 ||||| || || ||||| || |||||||| || ||||| || || |||||||||||||||||| || ||||||||||||||||||||||||| || ||||||  || |   | | ||  | | |  | |   ||||| | |||    || || | ||   ||   |||    | |    | | ||      | |   ||      
GATGAGCGCCTCTAGGTTTATAAAGTGCGTTACGGTCGGTGATGGTGCTGTCGGCAAAACCTGCATGCTGATTTCCTACACCAGCAACACTTTCCCTACGgttagttccccattttctgattctaggtttttgtatctttggtt---cttggaaagat---cgagggaaagcaagaggaaccaaaagaaaatgctctaaaagaaaa

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|31561454|gb|CD487292.1|CD487292
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|4396727|gb|AI495724.1|AI495724
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|120533487|gb|EH261620.1|EH261620
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|4313831|gb|AI460950.1|AI460950
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|193329761|gb|FK294493.1|FK294493
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCTACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGA
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCC-ACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGA
EST: gi|298164350|gb|HO013995.1|HO013995
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|16348169|gb|BI973764.1|BI973764
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|10845271|gb|BF068427.1|BF068427
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|6483101|gb|AW202293.1|AW202293
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|19269284|gb|BM885540.1|BM885540
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|17021451|gb|BM092485.1|BM092485
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|193378085|gb|FK344594.1|FK344594
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
EST: gi|19052868|gb|BM731535.1|BM731535
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcgataacagGACTACGTGCCCACGGTTTTTGACAATTTCAGTGCTAATGTTGTGGTGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGAGTGCATCGAGGTTCATTAAGTGCGTCACCGTCGGCGACGGCGCTGTCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttctttctcctcttcccaattataactatctgtagttaaaattagatatatatgcgtttgaattgtaaaactcctataatttggagtttccaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc