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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT

Basic information

species Glycine max
transcript GLYMA08G08920.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 7
gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
                              ||  |||  | |  ||  | || | ||  ||   |   || | || |    |   |  || ||||     |||| || |||||||| || ||||| || ||||| ||||||||  | |||||||||||||||||||| ||||| |||||||||||||| || || || |||||
-----------------------------gtaattattgaaacttgtttcatac-atatttgtttgattcttataggtctga---gcgatttcttgtggttagGTGAGAGAAGGCTGGAGGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAATGATCAGGACCGAGTGGCTAT

upper sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 7
gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
               |    || | |  | ||   |  |  || |||||   | |  |||| |        ||| | || |||||         |   |  |||||||||||||||||||||||| || ||||| ||||||||  | ||||| |||||||||||||| ||||| || |||||||||||||| || ||||||||
--------------gtaaattacacaactctactca-gtgcatgtgcattggtgtcgtattcctgtaaaagtctcatgacaaatt---------tctgttcagGGGAAAGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTCGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGACCGAGTTGCTAT

upper sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 7
gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttct-tctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
                            || || || | |  | | | || | | |||  ||    | |   ||    ||   |  |      ||| | |  ||||||  |||||||||||||||| || ||||| ||||||||  | |||||||||||||||||||| ||||| || ||||||||||||||||| ||||||||
---------------------------gtaaat-tacacaactctacttagtgc-attggtattcatatt-cctgtaaaagcctcatggcgagtttttgttcagGGGAGCGAAGGCTTGAAGCTGGTGCCATGGTTCTTGCTGATCGTGGTGTTGTCTGCATTGATGAGTTTGATAAAATGAATGATCAAGATCGAGTTGCTAT

upper sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 7
--gtaaatcattcgtcatgggctatatatatatatat-atata-tatatgcataattctatta----ttacatctgtcatctaagga-aaaattgtaatctctttcttct-agGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
    ||| ||  |   |  |  |  | || | | ||| | ||  || |  || ||||  |       | | |  ||  || |      |||||   | |||| || |  | ||||||| |||| || |||||||| |||||||| || ||||| | |||| | || |||||||| || ||||| |||||||||||||| || || ||||||||
gtaaaaagcacacaaaagcgtttccacatttttttatcaaatgctaaaatcaaaatttgaaggaaggtcaaaagtgctatttctcattaaaatcaaattctcattttcatcagGGGAACGAAGACTAGAAGCTGGTGCAATGGTCCTCGCTGATAAAGGTATCGTGTGCATTGACGAGTTTGATAAGATGAATGATCAGGACCGAGTTGCTAT

upper sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
                      || || ||| |    |     | ||||  |    |||||       |  |  |    |  ||| |  |  |||      ||| ||||||||||| |||||||| || ||||| ||||||||  |||||||||| || |||||||| |||||||||||||||||||||||||||||||||||
---------------------gta-atttatctcaccaggcccaagcatgttagcgttatttggcaattgcttcagactagtattctctttccttgtcatcagGAGAAAGAAGGCTAGAAGCTGGTGCCATGGTTCTTGCTGATCGAGGTGTTGTTTGTATTGATGAGTTTGACAAGATGAATGATCAAGATCGTGTTGCTAT

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|193648608|gb|FK599273.1|FK599273
EST:     CTTTCTTGGGGTTGGTTTGACAGCCGCAGTTACTTCAGATCAAGAAACAG                         GGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTG
genomic: C-TTC-TGGGGTTGGTTTGACAGCCGCAGTTACTTCAGATCAAGAAACAGgtaaatcatt ... tttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTG
EST: gi|193482813|gb|FK446596.1|FK446596
EST:     ACAGCCGCAGTTACTTCAGATCAAGAAACAG                         GGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTG
genomic: ACAGCCGCAGTTACTTCAGATCAAGAAACAGgtaaatcatt ... tttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTG
EST: gi|208029661|gb|GD832039.1|GD832039
EST:     TCTTCTGGGGTTGGTTTTGACAGCCGCAGTTACTTCAGATCAAGAAACAG                         GGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTG
genomic: TCTTCTGGGGTTGG-TTTGACAGCCGCAGTTACTTCAGATCAAGAAACAGgtaaatcatt ... tttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT
                                      taatctctttcttct  CT-rich tract
                              aaaaattgtaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcattcgtcatgggctatatatatatatatatatatatatgcataattctattattacatctgtcatctaaggaaaaattgtaatctctttcttctagGGGAAAGAAGGCTTGAAGCTGGGGCAATGGTGCTTGCTGACAGAGGTGTTGTCTGCATTGATGAATTTGACAAGATGAATGATCAAGATCGTGTTGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG