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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattttttcccctttttctaaattggtatgtgctgtggcaatggaaaacatggatttgtaatattttgtatgctacctccctcatttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTTTTGCAAGTGGAAGTCCATTCAGTAATGTGGATCTTG

Basic information

species Glycine max
transcript GLYMA03G24630.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G24630.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os07g31380.1 (Oryza sativa), 3'ss of exon 13
gtatgtattttttcccctttttctaaattggtatgtgctgtggcaatggaaaacatggatttgtaatattttgtatgctacctccctcatttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTTTTGCAAGTGGAAGTCCATTCAGTAATGTGGATCTTG
|| |||    ||     ||     ||| |    | |  | || ||    |    ||||| |  | || | |||         | ||  |||     |||||||||| ||  |||||||||| || || ||| | ||||| || || || ||||| |||||||| ||||| ||| ||||||||||||
gtttgtgcagttgtgttttaccacaaagttcattattttctg-catgccatctaatggactaatcatgtgttgg--------ttccatatt----acagCTGAATGTACACCTGAAGAAGCCTTTTCAATTCTTGGTGAAAAGATCATCTTTGCCAGTGGAAGCCCATTTAGTGATGTGGATCTTG

upper sequence: GLYMA03G24630.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0021g00500.t01 (Vitis vinifera), 3'ss of exon 13
gtatgtattttttcccctttttctaaattggtatgtgctgtggcaatggaaaacatggatttgtaatattttgtatgctacctccctcatttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTTTTGCAAGTGGAAGTCCATTCAGTAATGTGGATCTTG
                  | |  ||| |  |  ||        |  ||   | |  || ||  |||| || | | |  ||  |  ||  ||  || |||||||||||||| |||||||||| ||||||||  ||||||| ||  |||| |||||||||||||| |||||||   ||||||||||||
-----------------gtatagtaattcagactggttcacatctttg---acctaggcttcttaatcttatttttcttaaatatcttgtt--tgacagCTGAATGCACCCCTGAAGAAGCTTTCTCCATCGTGGGTGATAATGTTATATTTGCAAGTGGAAGCCCATTCAAGGATGTGGATCTTG
















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|8284122|gb|BE021681.1|BE021681
EST:     AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATG                         CTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
genomic: AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATGgtatgtattt ... tttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
EST: gi|58018827|gb|CX705569.1|CX705569
EST:     AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATG                         CTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
genomic: AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATGgtatgtattt ... tttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
EST: gi|58015662|gb|CX702404.1|CX702404
EST:     AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATG                         CTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
genomic: AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATGgtatgtattt ... tttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
EST: gi|9264573|gb|BE352720.1|BE352720
EST:     ACATCAACCCAGACCAGCCATATTTGCTATGTCAAATCCA-CAAAGAATG                         CTGAATGCACCGCTTGAAGAAGCATTCT
genomic: ACATCAACC-AGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATGgtatgtattt ... tttttggcagCTGAATGCACCGCT-GAAGAAGCATTCT
EST: gi|17401415|gb|BM178197.1|BM178197
EST:     AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATG                         CTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
genomic: AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATGgtatgtattt ... tttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
EST: gi|207738333|gb|GD716993.1|GD716993
EST:     AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATG                         CTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT
genomic: AACATCAACCAGACCAGCCATATTTGCTATGTCAAATCCAACAAAGAATGgtatgtattt ... tttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggaaaacatggatttgtaatattttgtatgctacctccctcatttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTTTTGCAAGTGGAAGTCCATTCAGTAATGTGGATCTTG
                                 ctacctccctcatttt  CT-rich tract
              atttgtaatattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattttttcccctttttctaaattggtatgtgctgtggcaatggaaaacatggatttgtaatattttgtatgctacctccctcatttttggcagCTGAATGCACCGCTGAAGAAGCATTCTCCATTTTGGGTGACAACATTATTTTTGCAAGTGGAAGTCCATTCAGTAATGTGGATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG