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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaaccatatttcacattaaggttatattagtatctataatttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA

Basic information

species Glycine max
transcript GLYMA19G24620.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 4
-----tttaaaccatatttcacattaaggttatattagtatctataatttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
       ||  |  |   || ||  ||  |  | |||    |||  |    ||  |   |     || |   |||||     ||  |  | || |  |||  ||| ||||| ||||| ||||||||||||||| |||| ||||| || |||||||| ||||| || || ||||| || |||||||||||||| || || || |||
atcacaatattcttttgctcccaagaaaatccttttaaccactactaccctattcttgctgtttactcattgtctta---tatttgaacacttct--atgatcagTATTCGGCGTGGACATCAAGTTTATACACAAGTGTGTGCCTCTTGCCATTCCATGTCATTAATTTCGTACCGAGATTTGGTTGGTGTGGCCTACACTGAA

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g70960.2 (Oryza sativa), 3'ss of exon 3
tttaaaccatatttcacattaaggttatattagtatctataattta-ataataattaacgccttaaattcttaatgctttcaatt-aatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
      ||||  | |  |   ||  | |     | |   |  || | ||  | ||     | || |  |||| ||   || | || ||      ||| |||| ||  | ||||| ||||||||||||||| |||| ||||| || || || || ||||| ||||| || || || |||||||||||||| || |||||||||
--atgcccatgctgctgaggtagtcttttgagctgttcttttttcatatttttatcttttctttcacctctttatttatttattttaaaaacatatgagcagAATAAGGCGTGGCCATCAAGTTTATACACAAGTGTGTGCCTCTTGTCACTCAATGTCCTTGATTTCATACCGAGATTTGGTTGGTGTGGCCTATACAGAA

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 3
tttaaaccatatttcacattaaggttatattagtatctataatttaataataattaacgccttaaatt--cttaatgctttcaattaatttttcat-gggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
||||     | | |    |  ||| || |||  | |  |     || ||     |       ||  ||    ||||   |   || ||  | | || |  ||| ||||| || || ||||||||||| ||| |||| |||||||| || || || ||||| ||||| || || |||||||||||||| || || ||||| || 
tttagt---tgtcttgtttctaggataaattcttgttgaagtgctagtaccttgttttcttgtatgttgctctaatttatcttataaaaatattattgcacagAATTCGCCGAGGGCATCAAGTTTACACACAAGTTTGTGCTTCTTGTCACTCCATGTCCTTGATTTCATACCGTGATTTGGTTGGGGTGGCCTATACTGAG

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 3
-tttaaaccatatttcacattaaggttatattagtatctataatttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
    |||     | ||    ||   | |||||||  | |  || || |    ||||   |   |  ||   | ||        || || ||  ||| ||||||| |||||||| ||||||||||||    |||||||||| || |||||||| |||||| |||| || || || || ||||| ||||| || || ||||| 
aaagaaagtgactatcctgctaccctaatattagactgtgaaacttcagtgaaatttttgtactgtatgaattat-tgaaaggttgatgttgtatgagcagGATCCGTCGTGGGCATCAAGTTTATCAGCAAGTCTGTGCATCATGCCATTCAATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTCGCCTACACAGAG

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 2
-------tttaaaccatatttca--cattaaggttatattagtatctataatttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
       || || | | | ||||  ||| |  || | |||   |     || || | ||| |   |    | | | |  |  | ||  |  || |||| | ||| ||||||| ||||||||||| |||||||||    |||| ||||| || |||||||| |||||| |||| || || || || ||||| |||||||| || ||||| 
gtgagtgttcaagctacaattcaatcatcatagtgaaattgcaacactaaagttgaaaattagagaaatttgagactgctt-tactgacggttgatttgtaatgagcagGATCCGTCGTGGTCACCAAGTTTATCAGCAAGTTTGTGCGTCTTGCCATTCGATGTCTCTGATCTCATACCGAGACTTGGTGGGTGTTGCCTACACAGAG

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 3
tttaaaccatatttcacattaaggttatattagtatctataat--ttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
||| | |  ||| |      ||  || |  |  |||||    |  |||||  | ||       |   | |   | |  ||| |    | |||   || ||||||||||||||||||| || |||||   | |||||||||| |||||||||||||||||  | || || ||||||||||| || ||||| || |||||||||
tttgatc--tatctagggccaaactttttgttatatcttgggtcattaatcttgatatcaatttctcaatgcaactttttttatgccaatttatttgagcagGATTCGTCGTGGTCACCAGGTTTACCAACAAGTCTGTGCATCCTGCCATTCTATGTCACTAATTTCATATCGTGATTTAGTGGGTGTGGCATATACAGAA

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|19348486|gb|BM893027.1|BM893027
EST:     AGCTATCCGTGGCCTCACAAAGGAATTCTTAGTTCATATGATCATGCTTC                         GATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTC
genomic: AGCTATCCGTGGCCTCACAAAGGAATTCTTAGTTCATATGATCATGCTTCgtaagtttgg ... tcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTC
EST: gi|192326431|gb|FK017703.1|FK017703
EST:     AGCTATCCGTGGCCTCACAAAGGAATTCTTAGTTCATATGATCATGCTTC                         GATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTC
genomic: AGCTATCCGTGGCCTCACAAAGGAATTCTTAGTTCATATGATCATGCTTCgtaagtttgg ... tcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTC
EST: gi|254330991|gb|GR842256.1|GR842256
EST:     AGCTATCCATGGCCTCACAAGGGAATTCTTAGTTCATATGATCACGCTTC                         GATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTC
genomic: AGCTATCCGTGGCCTCACAAAGGAATTCTTAGTTCATATGATCATGCTTCgtaagtttgg ... tcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA
                                         tttttcat  CT-rich tract
                ttaaattcttaatgct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaaccatatttcacattaaggttatattagtatctataatttaataataattaacgccttaaattcttaatgctttcaattaatttttcatgggcagGATTCGTCGTGGTCATCAAGTTTATACAGAAGTCTGTGCTTCCTGCCATTCTATGTCTTTGATATCGTATCGTGATTTGGTTGGTGTTGCTTATACAGAA

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