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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt...

Basic information

species Glycine max
transcript GLYMA14G04520.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatccc---ctctctctgtgtgtgtgtgtg-tgtgttgttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt
 |||||| | |   || || ||||||||||| ||||| ||||| | |||||| || |||||||||||||||||| |||  |||||||| ||||| ||| |||  ||  |||   | ||| ||   | |    | | || | |||    | |      | |    |  | |||||||   | |||     |     |||      
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgaccctctccctccctccctctcctcgcgctgcgctgtactgtacgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc----

upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g17250.1 (Oryza sativa), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattg-ttactatctgttacttttatttatttatattactgctatcagtttt
|||||||      ||| |||||||||||||| || || ||||| | |||||| || |||||||||||||||||| |||  | |  ||| ||||| ||| |||  |    ||  | | |           |     |   | ||   || |  ||  ||||| | |    ||||  |   |    |   | ||     | ||
CGGACCCCCGGGGCGTGCTCCAGAGCTGGGACCCGACCCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGCCGGCCGCGTCACCCGCCTgtgagtccacctcccccccccccaccgccgccgccgcc-tcgccgactgagctggctactaccggccggttttgctccctccgttgtgtactgcttttgtt

upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G121820_T01 (Zea mays), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattgttactatctgttacttttatttatt-tatattactgctatcagtttt-
 |||||| | |  |||||| ||||||||||| ||||| ||||| | |||||| || |||||||||||||||||| |||  |||||||| ||||| ||| |||  ||   |||   ||||     | |   | | | | |   | || |     |   |    | | | |           |    |   | |        | 
GGGACCCCGGCGGCGTTCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACCCGCCTgtgagccgtccccgcctctcaac-tctccctctttctcggccccttttcccccgcggcccgtt-tgagtcgggcccgccgtggcgtgtggatggggagcata

upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM5G815009_T01 (Zea mays), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt------
 |||||| | |  ||| || ||||||||||| ||||| ||||| | |||||| || |||||||||||||||||| |||  |||||||| ||||| ||| |||  ||  |  | ||| |           ||    | |    | ||         | |   | |   | || | | ||   | | || |     |  ||       
GGGACCCCGGCGGCGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACCCGCCTgtgagccgctgc-ctcccaactctccctcgtcctcgctcccccctttccc----ctgcggcccgcccccttcaataatccct-tgacggggggaaacttcagtatg

upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G21090.1 (Arabidopsis thaliana), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt
| || || ||| | || ||||||||||||||||| ||||| ||||  || ||||| |||||||| |||||||| ||||| |||||||| |||||||| ||||| |   | | | |||||       ||| |       |||| ||    ||   |   |     ||   || ||  | |   |    |    ||  ||| 
CAGATCCAGACCATGTCCTCCAGAGCTGGGATCCAACTCTTGTTAATCCTTGTACCTGGTTCCATGTCACCTGTAACCAAGACAACCGCGTCACTCGTGTgtaagatcctcttttctcttatctcctgttttgaacaagttgattcgccaagaatctgtggagattctattgatacagtctgaaatttttgctctattta

upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv08s0040g00520.t01 (Vitis vinifera), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgtt-gttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt
| || || |||||||| ||||||||||||||||| |  ||||| | ||| ||||| ||||||||| ||||||| || ||||||  ||| |||||||| ||||||| || | || ||| | ||    | | |  || || ||| | ||| | ||   ||   |   |  |   | |||||||||||   |  |      || 
CCGATCCGGACAACGTGCTCCAGAGCTGGGATCCGAACCTCGTCAACCCTTGTACCTGGTTCCACATCACCTGTAATCAGGACGGCCGCGTCACTCGAGTgtatgtattctctatctttctgctactctcttagttttcgtttcgttcctgatatataggtttcatctcgagtttttatttatatatttatttctccctt-

upper sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv06s0009g01210.t01 (Vitis vinifera), 5'ss of exon 1
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattgttactatctgttacttttatttatttatattact---gctatcagtttt
| || || || ||||  || |||||||||||||| || |||||||  || || |||||||| || |||||||| ||||||||||| || || ||||| ||||||      | || ||||| |  | | | | ||| || || ||||||| ||| || |  |  | |   |||  ||  | | |  | |   |  || || |  
CAGATCCGGATAACGCCCTTCAGAGCTGGGATCCAACCCTCGTTAATCCTTGCACTTGGTTTCATGTCACCTGTAACCAGGACAATCGCGTTACTCGAGTgtatcttcttcttcactctgcgcctttctttctgttttttttctttcttcatt-ttcccttaggctctgtttgcttcctgacagcatttgggaaataaggt--

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|193429641|gb|FK393637.1|FK393637
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|23063666|gb|BU578586.1|BU578586
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|16347934|gb|BI973529.1|BI973529
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|37995157|gb|CF806746.1|CF806746
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|298196158|gb|HO044549.1|HO044549
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|15203476|gb|BI426244.1|BI426244
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|7587949|gb|AW703755.1|AW703755
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|4291420|gb|AI441759.1|AI441759
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|15814273|gb|BI786548.1|BI786548
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|19053727|gb|BM732394.1|BM732394
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|37996287|gb|CF807876.1|CF807876
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|58025114|gb|CX711855.1|CX711855
EST:     TGTACTTGGTTCCACGTCACNTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|192326528|gb|FK017275.1|FK017275
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|7589724|gb|AW705492.1|AW705492
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGNGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|213589334|gb|DB961667.1|DB961667
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|15815888|gb|BI788163.1|BI788163
EST:     CTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: CTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|7924480|gb|AW830506.1|AW830506
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGTGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|24135865|gb|BU926375.1|BU926375
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|23056915|gb|BU577818.1|BU577818
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|16106312|gb|BI894052.1|BI894052
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|26057238|gb|CA800152.1|CA800152
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|13790989|gb|BG653580.1|BG653580
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|27424142|gb|CA935662.1|CA935662
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|4396381|gb|AI495378.1|AI495378
EST:     TACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCAC-CTGCGGT                         GGATCTTGGTAACTCTAACCT
genomic: TACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTC-GCG-Tgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCT
EST: gi|298185858|gb|HO031019.1|HO031019
EST:     GTCACTCGCGT                         GGATCTTGGTAACTCTAACCTATCTGGACACTTGGTACCTGAACTTGGGAA
genomic: GTCACTCGCGTgtatgcatcc ... ttttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatcccctctctctgtgtgtgtgtgtgtgtgttgttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt

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