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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaaaaatagtatgacatctttctctcctctgtctaaattagttagttagctggttaagtgttttctttatcttattgctatctaaacctatttgatgaacatcttagtgtacttggcgaagttatttaacaGAGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCAGGCTACC

Basic information

species Glycine max
transcript GLYMA18G44940.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G44940.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g40260.1 (Oryza sativa), 3'ss of exon 4
--ggtaaaaatagtatgacatctttctctcctctgtctaaattagttagttagctggttaagtgttttcttt--atcttattgctatct----aaacctatt--------tgatgaacatcttagtgtacttggcgaagttatttaacaGAGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCAGGCTACC-
  | | |      | |  |||  ||  |  ||| || ||   |  | ||   | | || ||      ||||   |||| |    ||| |    |||   |||        |||||||||||||||||||||||  |||||||||| ||||||||  | ||   ||||  | ||||||| ||||| || || || || ||||||||||| ||||| || ||||||||||| || ||||| ||    || | 
gtgcttacctcgttgtttcattattagcggctc-gtttatgatcctaagc--gttagtcaaaccacatcttctaatctgaagattatttgcagaaattcatttttctagatgatgaacatcttagtgtacttgtagaagttatttgacagAGGGAGAAGAGAGGAAGCAACTAATTGGTATGGCGCGAGCAACTTCAGACCATGCCTTTAATGCTACCATTTGGGATGTTCTCGTTGACCCTTCATATCA

upper sequence: GLYMA18G44940.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g00580.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------ggtaaaaatagtatgacatctttctctcctctgtctaaattagttagttagctggttaagtgttttctttatcttattgctatctaaacctatttgatgaacatcttagtgtacttggcgaagttatttaacaGAGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCAGGCTACC-
                                                  ||| |   |||  |   ||||  | ||  | | |  |    |      |  ||| || ||| || | | ||| |  ||  | | |    |   | |||||     | | | |||||||  ||||||||| |||||| ||||||| || ||||   | |||||||||||||||||||| || || |||||||||||||||||||||||||||||||| ||||||||    || | 
gtacttactaaatatgatgttgttacattactctccaattcattacgattggttatgttagattagtatctg-cacttgtttattcatccaaaactacttactg-ttgagt-ttatttctatttctttttttttttcctcatatagatga-----tgaatatacttggaaaagttatttgacagAGAGGAATGAGCAAAAGAAGCTTATTGGCATGGCCCGTGCTACATCAGATCATGCCTTCAATGCCACAATTTGGGATGTCCTTGTTGATCCTTCATATCA

upper sequence: GLYMA18G44940.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S332_23V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------ggtaaaaatag--tatgacatctttctctcctctgtctaaattagttagttagctggttaagtgttttctttatcttattgctatctaaacctatttgatgaacatcttagtgtacttggcgaagttatttaacaGAGGGGAATGAACAGA------------------AGAGA--------TTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCAGGCTACC
                                                 ||  |  |||    |||   | |    || |   ||   | |  ||   | ||    |   | |||  ||||| |||||  | | ||||  ||||  |        ||  |   |||     | ||||  |  |    |||| |||||||                  |||||         | |||||||||||||| ||||| |||||||| ||||||||||| || |||||||| || || || ||           
gtaaccttctaactcgaacctcgttttgttgtacatccttgttattattgtccatgtagaccttgaagccatgtgttctttaatccgcact--ttcacttgcaaagtcgctttttattttattttatttat-tttaaatgtattcaacatgacgattcatactcttccttgaattatggactatgatggaaggaacagATGGTGAAGATCCCGTTGTAGAGAAGCGAGAACTTATTGGCATGGCCCGGGCTACATCTGACCACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGA-----------

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|6915559|gb|AW397089.1|AW397089
EST:     ATAGTTATATAGTAGCCTCACTACATTCTATAAGAAAGTCACATGGGTCA                         GAGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGAC
genomic: ATAGTTATATAGTAGCCTCACTACATTCTATAAGAAAGTCACATGGGTCAggtaaaaata ... ttatttaacaGAGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatctaaacctatttgatgaacatcttagtgtacttggcgaagttatttaacaGAGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCAGGCTACC
                                          aagttatttaa  TA-rich tract