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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgacattattatcatttaatcttatgctcttatagctttgagagaatacatgaacatttttggtatatctactgggagttctggctcatttgatctttctgtgacttacaattgaattaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAGGATGGGG

Basic information

species Glycine max
transcript GLYMA09G33160.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G057037_T01 (Zea mays), 3'ss of exon 3
gtgagtgacattattatcatttaatcttatgctcttatagctttgagagaatacatgaacatttttggtatatctactgggagttctggctcatttgatctttctgtgacttacaattgaattaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAGGATGGGG
                             |  | |||   |||| |    ||     |||||  ||  | |  ||  ||       |   | |||  |  | | | |   |||   ||  |          ||||||   | |  |    ||||| ||||| || ||||||||||| || |||||||||||||| ||||||
----------------------------gtaat-ttacttcttttatgtgatgatgaaacatagttcctcttcctgttgaagaaattaattaattaaacatcttt-tattttaatgttagA----------ATTACCTCTGGAACCAAGTGGATACATCCAAGTATTTCTTGATGGTGGATTGAACCAACAAAGAATGGGG
















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|9899441|gb|BE608409.1|BE608409
EST:     ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAA                         CATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
genomic: ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAAgtgagtgaca ... attaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
EST: gi|18734891|gb|BM528445.1|BM528445
EST:     ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAA                         CATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
genomic: ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAAgtgagtgaca ... attaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
EST: gi|19053956|gb|BM732623.1|BM732623
EST:     ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAA                         CATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
genomic: ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAAgtgagtgaca ... attaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
EST: gi|15288236|gb|BI472127.1|BI472127
EST:     ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAA                         CATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
genomic: ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAAgtgagtgaca ... attaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
EST: gi|308098228|gb|HO759969.1|HO759969
EST:     ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAA                         CATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
genomic: ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAAgtgagtgaca ... attaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
EST: gi|120534087|gb|EH262220.1|EH262220
EST:     ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAA                         CATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT
genomic: ACCTCTGGAAAGCCAAGGATGGAAACCTTATGTTGAATCAAATAAGCCAAgtgagtgaca ... attaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgggagttctggctcatttgatctttctgtgacttacaattgaattaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAGGATGGGG
                                gacttac  putative branch site (score: 2)
                                   ttacaattgaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgacattattatcatttaatcttatgctcttatagctttgagagaatacatgaacatttttggtatatctactgggagttctggctcatttgatctttctgtgacttacaattgaattaaagcagCATTACCAGAGAAGTCCGAGGGATATATCCAGGTCTTTCTTGATGGAGGTTTGAACCAACAAAGGATGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG