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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCCAACTATGAGAAGGAACTGGAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtttacgaaaatactatcatgaacattaattagagtatatgagaaaaatgtttaattcattttcctcctccatgtataatag

Basic information

species Glycine max
transcript GLYMA17G07010.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07010.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G086573_T01 (Zea mays), 5'ss of exon 6
ATTTCCAACTATGAGAAGGAACTGGAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtttacgaaaatactatcatgaacattaattagagtatatgagaaaaatgtttaattcattttcctcctccat-gtataatag-----------
 || |  | |||||||||||  | ||||||||||||||||||||  | ||||||||||||||||| ||||| |||| |    | | |    || || | |  ||||  |||     |      | |  || || |  |   ||    | | ||| || | || |           
GTTGCTGAGTATGAGAAGGAGGTCGAGGAGATGAAGAACATGACGCGACAAGAGTTTGTTGCTTCCCTTCGAAGgtgatcactgttctgtgatgctgtaac-aacaacaatagtccttagcttgcaggattttcagatagcttaatgcatgcattgtttgattgttatatgcata

upper sequence: GLYMA17G07010.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 5'ss of exon 6
ATTTCCAACTATGAGAAGGAACTGGAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtttacgaa----aatactatcatgaacattaattagagtatatgagaaaaatgtttaattcattttcctcctccatgtataatag-
 |||| ||||||||||| ||||| ||| | ||||||||||||||||||||||||||||||||||| ||  | |||||||   |     ||    |||  |  |||   | |   ||  |    | |  |   ||    ||||  || | ||  |   | | |      
GTTTCTAACTATGAGAAAGAACTTGAGAATATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCACTCAGAAGgtaaacaatcactcaattcaaatttttgcattctcttcctttttatgtcaagccatgcattcaaaattttttctgcttttttttttctctccag

upper sequence: GLYMA17G07010.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 5'ss of exon 5
ATTTCCAACTATGAGAAGGAACTGGAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtttacgaaaatac----tatcatgaacattaattagagtatatgagaaaaatgtttaattcattttcctcctccatgtataatag--------
 ||   |  || ||  | || ||||||||||||||||||||| || |||| |||| |||||| ||  |  | ||||  |||  ||  | |  | |    || |||   |     ||    ||  || ||    |||  |      |||     ||   |    |  |        
CTTGATACATACGAACAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTTGCCTCGTTGAGAAGgtgcaatccttgaggagtttcctgataacatagtcga-ggttgatatagttgtgatttgtgtccacaagggttttgagttcagggacagactgtgagagat

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|7685789|gb|AW756437.1|AW756437
EST:     GAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAG                         GAAGAGCAGTGGT
genomic: GAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtt ... tgtataatagGAAGAGCAGTGGT
EST: gi|14259589|gb|BG882497.1|BG882497
EST:     GAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAG                         GAAGAGCAGTGGTTTCTCTAGAGGGGCCTCTATATACAGAGGAGTAACGAG
genomic: GAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtt ... tgtataatagGAAGAGCAGTGGTTTCTCTAGAGGGGCCTCTATATACAGAGGAGTAACGAG
EST: gi|14259710|gb|BG882618.1|BG882618
EST:     GAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAG                         GAAGAGCAGTGGTTTCTCTAGAGGGGCCTCTATATACAGAGGAGTAACGAG
genomic: GAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtt ... tgtataatagGAAGAGCAGTGGTTTCTCTAGAGGGGCCTCTATATACAGAGGAGTAACGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCCAACTATGAGAAGGAACTGGAGGAGATGAAGAACATGACTAGGCAAGAGTTTGTTGCTTCTCTTCGTAGgtaaaatgtttacgaaaatactatcatgaacattaattagagtatatgagaaaaatgtttaattcattttcctcctccatgtataatag

- - - - - - - - - - - - GAGGAG
- - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - -  GCAAGA