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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacctgttcttggaaggaaaaaaaaggaggaaagaaaatgcttgcttgaactactagtatagaaaatcacatcttaagtcattgtcatctgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAACAATGTTGAGACTTCTGGCATGCGGTTTGACTCTAATGCAAGAACTGCAT

Basic information

species Glycine max
transcript GLYMA09G27430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G27430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g02340.t01 (Vitis vinifera), 3'ss of exon 2
acacctgttct-tggaaggaaaaaaaaggaggaaagaaaatgcttgcttgaactactagtatagaaaatcacatct-taagtcattgtcatctgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAACAATGTTGAGACTTCTGGCATGCGGTTTGACTCTAATGCAAGAACTGCAT
 | |  ||| | |  | |      | |     || |  |||   |  ||   | | |   | ||| |||  || || | | |  ||    ||||| | | ||||||| |  ||||| |||||  | ||||||||||||||||| ||| | ||||||||  | | ||||||||||||||||||    | |||||| |||||| 
-ccctggttttctacatgtggtggataattccaatgtcaatagctcattaccccaatttca-agacaatttcagctgttaattttttctgtctgtatctcagGTTGGCGATGATGAGTTTGGTCATATGTTGGCTGACATTTTGAAGAAAAACAATGTCAACAATTCTGGCATGCGGTTTGATCACAGTGCAAGGACTGCAC

upper sequence: GLYMA09G27430.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_283V6.1 (Physcomitrella patens), 3'ss of exon 2
acacctgttcttggaaggaaaaaaaaggaggaaagaaaatgcttgcttgaactactagtatagaaaatcacatcttaagtcattgtcatctgtt--tattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAACAATGTTGAGACTTCTGGCATGCGGTTTGACTCTAATGCAAGAACTGCAT
 |     ||| | | |||  ||    | | |    |         ||   | |  |     |  |||  | |   | | | |   |  | || |    |||||||||||  ||||||||||||||||||||||  ||  | || ||  ||||||  || || ||    |     || |||||  | ||||| || |||||| 
tcgttgcttccttgcaggctaat--tgcatgccttatgccttaacctcccatttttccatgaagaaacaaaagactcactgaagcttgtttgatggcgttagGTTGGAGATGATGAATTTGGGTACATGTTGGTGGAGGTGTTGAAAGAGAACAGAGTGGAAACAAAAGCTTGTCGCTTTGATCCAAATGCCAGGACTGCAC
















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|5057912|gb|AI736388.1|AI736388
EST:     GGTATCTCTAGACTAGGAAGTTCATCTGCTTTCATAGGCAAG                         GTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAAC
genomic: GGTATCTCTAGACTAGGAAGTTCATCTGCTTTCATAGGCAAGgtgtagtttt ... tgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAAC
EST: gi|209708552|gb|BW668165.1|BW668165
EST:     TGGCTGTTGGTATCTCTAGACTAGGAAGTTCATCTGCTTTCATAGGCAAG                         GTTGGAGCAGATGAATTTGGGTACATGTTGGCTG
genomic: TGGCTGTTGGTATCTCTAGACTAGGAAGTTCATCTGCTTTCATAGGCAAGgtgtagtttt ... tgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTG
EST: gi|298167876|gb|HO013139.1|HO013139
EST:     TGGCTGTTGGTATCTCTAGACTAGGAAGTTCATCTGCTTTCATAGGCAAG                         GTTGGAGCAGATGAATTTGGGTATATGTTGGCTGACATTTTAAAGCAGAAC
genomic: TGGCTGTTGGTATCTCTAGACTAGGAAGTTCATCTGCTTTCATAGGCAAGgtgtagtttt ... tgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaactactagtatagaaaatcacatcttaagtcattgtcatctgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAACAATGTTGAGACTTCTGGCATGCGGTTTGACTCTAATGCAAGAACTGCAT
                                           tctgttt  CT-rich tract
             tatagaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacctgttcttggaaggaaaaaaaaggaggaaagaaaatgcttgcttgaactactagtatagaaaatcacatcttaagtcattgtcatctgtttattagGTTGGAGCAGATGAATTTGGGTACATGTTGGCTGACATTTTAAAGCAGAACAATGTTGAGACTTCTGGCATGCGGTTTGACTCTAATGCAAGAACTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
-cacctgt
- - - - - -tggaagg
- - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatc