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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgaatatatttggttgttagtgcatcaaaatgatatttcctaactatatttgctgattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT

Basic information

species Glycine max
transcript GLYMA11G08390.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 18
gtacttgaatatatttggttgttagtgcatcaaaatgatatttcctaactatatttgctgattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT
         ||| ||||  || || ||| | |   | ||| ||| | |   || |  |||||| | || ||  |||           ||||||| ||||||||||| ||||| || ||||||||||| || || || ||||| |  ||| ||||||||||||||||  | 
--------gtatgtttg--tgatactgcgt-attttcataattcttcatcttactctctgattatgtttttaattt-----------agGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 17
gtacttgaatatatttggttgttagtgcatcaaaatgatatttcctaactatatttgctgattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT
         |||  |||  |  || |||||    ||    |||  ||| | |   | || ||| |  || || | ||||||| ||| ||||||| ||||||||||| ||||| || ||||||||||| || || || ||||| |  ||  ||||||||||||||||| | 
--------gtatgcttg--taatactgcat----at----ttttgtaagtcttcct-cttattat-ctgattatgtttcttg-atttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATATTATATGAAGAAGAAATTGCG

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 17
gtacttgaatatatttggttgttagtg-catcaa--aatgatatttcctaactatatttgct-------gattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT
|||| ||| ||| ||| ||  | |    |||      |  || |  |  | |||| || |||       |  | |  | |||  |||| |   ||  ||||||||||||| ||||| ||||| |||||||||||||||||||||||||||||||| ||  | ||||||||||||||| | 
gtacatgagtatgttttgtgttaaaaatcattggtggaccatgtaacaaagctatgttagctctaaccagcatcttctttttgattttgtaatatacagGCTGCAAATGATTGTGATTTGGAACCTGTTGCTTATGAATTTTTCACCCAAGCTTACATATTGTATGAAGAAGAAATTGCG

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|15204547|gb|BI427315.1|BI427315
EST:     GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAG                         GCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
genomic: GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAGgtacttgaat ... ttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
EST: gi|192323264|gb|FK015270.1|FK015270
EST:     GTGTCCTGGCACCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAG                         GCTGCAAATGACTGTGAATTGGAACCTGTTGCTTATGAATTTTTCACCCAA
genomic: GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAGgtacttgaat ... ttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
EST: gi|193716713|gb|FK654271.1|FK654271
EST:     GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAG                         GCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
genomic: GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAGgtacttgaat ... ttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
EST: gi|7327057|gb|AW620855.1|AW620855
EST:     CAATGTGCTGAG                         GCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
genomic: CAATGTGCTGAGgtacttgaat ... ttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
EST: gi|14011053|gb|BG725975.1|BG725975
EST:     GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAG                         GCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
genomic: GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAGgtacttgaat ... ttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
EST: gi|12773342|gb|BG238269.1|BG238269
EST:     GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAG                         GCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA
genomic: GTGTCCTGGCGCCAGAATTAGCATTGCAGTTGTACTTGCAATGTGCTGAGgtacttgaat ... ttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatatttcctaactatatttgctgattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT
                           ttttattgtttctttt  CT-rich tract
                          attttattgtttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgaatatatttggttgttagtgcatcaaaatgatatttcctaactatatttgctgattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA