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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATTAGAAGGGCGCATGCTATTCATCCAATTACTGCTCTGCAAATGGAGTGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgctgcactttgcacattatttggattggattggatcatgattcatatcatacctttaataacttctgccaaacaacaaaatcaagcttgtaa...

Basic information

species Glycine max
transcript GLYMA10G30360.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30360.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0030g02020.t01 (Vitis vinifera), 5'ss of exon 4
CAATTAGAAGGGCGCATGCTATTCATCCAATTACTGCTCTGCAAATGGAGTGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgt---aaatttgctgcactttgcacattatttggattggattggatcatgatt-catatcatacctttaataacttctgccaaacaacaaaatcaagcttgtaa
|||| || ||||| |||||  ||||||| ||||||||  ||||||||||||||||||| ||| | || || ||||| ||  || |  | || ||||||||||   | |||   | |    | |  | | | |   ||   || |  |||  || | | | ||   ||||     |  ||   |     ||  || |  ||    
CAATAAGGAGGGCTCATGCAGTTCATCCCATTACTGCCTTGCAAATGGAGTGGTCCCTCTGGACCCGCGATATTGAGGAAGAAATAGTCCCTCTTTGCAGgtttcatattccatcctaagttctaaatctatctcttcacttagtccatccttgccttttatctgtttacatgttagtgttca--tgtaacttccaaattcc--

upper sequence: GLYMA10G30360.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0030g01990.t01 (Vitis vinifera), 5'ss of exon 4
CAATTAGAAGGGCGCATGCTATTCATCCAATTACTGCTCTGCAAATGGAGTGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgt---aaatttgctgcactttgcac---attatttggattggattggatcatgattcat--atcatacctttaataacttctgccaaacaacaaaatcaagcttgtaa-------------
|||| || ||||| |||||  ||||||| ||||||||  |  |||||||||||||||||||| |||| |||||||||||  || | || |||||||||||||     |||| ||   |||  |     ||| | |    |  |       ||  ||| |  || | | | |||||      |     |  ||    | |  ||||  |             
CAATAAGGAGGGCTCATGCAGTTCATCCCATTACTGCCATAGAAATGGAGTGGTCCCTTTGGACTCGAGAAATTGAAGAAGAAATTCTCCCACTTTGCAGgtttcgtatttcctatccttaacgattgattttctatcataaaacattctatagttcttgcattagatccttaat---ccttaatggaggacttggttacacttgggatatatttttatag

upper sequence: GLYMA10G30360.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0030g02060.t01 (Vitis vinifera), 5'ss of exon 4
CAATTAGAAGGGCGCATGCTATTCATCCAATTACTGCTCTGCAAATGGAGTGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgt---aaatttgctgcactttgcac---attatttggattggattggatcatgattcat--atcatacctttaat----aacttctgccaaacaacaaaatcaagcttgtaa-------------
|||| || ||||| |||||  ||||||| ||||||||  |  ||||||||||||| |||||| |||| |||||||||||  || | || |||||||||||||   | |||| ||   |||  |     ||| | |    |  |       ||  ||| |  || | | | |||||    ||    |     |  ||    | |  ||||  |             
CAATAAGGAGGGCTCATGCAGTTCATCCCATTACTGCCATAGAAATGGAGTGGTCTCTTTGGACTCGAGAAATTGAAGAAGAAATTCTCCCACTTTGCAGgtttcatatttcctatccttaacgattgattttctatcataaaacattctatagttcttgcattagatccttaatccttaatccttaatggaggactcggttacacttgggatatatttttatag

upper sequence: GLYMA10G30360.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0030g02050.t01 (Vitis vinifera), 5'ss of exon 4
CAATTAGAAGGGCGCATGCTATTCATCCAATTACTGCTCTGCAAATGGAGTGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgctgcactttgcacattatttggattgga---ttggatcatgattcatatcatacctttaata-acttctgccaaacaacaaaatcaagcttgtaa-
|||| || ||||| |||||| ||||||| ||||||||| | ||||||||||||||||||||| | ||||||||||| ||  || |  |||||||||||||||    ||  |  | | |   || | ||       ||   || |  | |  |||||  |||  |||   || | ||     | |   |    || |  || |   
CAATAAGGAGGGCTCATGCTGTTCATCCCATTACTGCTTTACAAATGGAGTGGTCCCTTTGGACCCGTGAAATTGAGGAAGAAATTGTTCCACTTTGCAGgt----ttcatatattctagccaatgttcttgcatgaccctttgtccttagttcat-ccatgtcttctctatagtttatttacatgtcggtttccatgttatccg

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|18711607|gb|BM522601.1|BM522601
EST:     TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgc ... acttttacagGGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
EST: gi|151402721|gb|EV272534.1|EV272534
EST:     TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgc ... acttttacagGGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
EST: gi|192300845|gb|FG991167.1|FG991167
EST:     TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgc ... acttttacagGGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
EST: gi|42722877|gb|CK768776.1|CK768776
EST:     TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAG                         GGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT
genomic: TGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgc ... acttttacagGGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATTAGAAGGGCGCATGCTATTCATCCAATTACTGCTCTGCAAATGGAGTGGTCCCTTTGGTCTCGTGAAATTGAAGATCAACTCCTTCCACTTTGCAGgtaaatttgctgcactttgcacattatttggattggattggatcatgattcatatcatacctttaataacttctgccaaacaacaaaatcaagcttgtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA