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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGAGCTGTAGTCAACATGATTGTCTCAAAGTATCCCACTATTAAGGGCATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaattgaatcatcatcatgtcaaatttagaggtcctgcttatattagatcacttaccattgtcaattagtcataagttgttatatgttggttaatattgtttgactaatggttacctaacatcaaaattggcattgatattttttattag

Basic information

species Glycine max
transcript GLYMA04G40580.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40580.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv16s0098g00850.t01 (Vitis vinifera), 5'ss of exon 2
ACTGGAGCTGTAGTCAACATGATTGTCTCAAAGTATCCCACTATTAAGGGCATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaattgaatcatcatcatgtcaaatttagaggtcctgcttatattagatcacttaccattgtcaattagtcat---aagttgttatatgttggttaatattgtttgactaatggttacctaacatcaaaattggcattgatattttttattag
||||||||     | ||||||||  | || || || |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| ||||  ||        ||  ||||||   | | |||      |||| ||   |   |||   |   |  |  |    ||||    | | |  | | |  |||| |  ||                                                    
ACTGGAGCCACCCTTAACATGATCATATCCAAATACCCCACTATTAAGGGCATTAACTTTGACTTGCCTCATGTTATTGATGATGCCCCATCTTATCCTGgtacatt--------tccacatcattctacaattaattcatctgcataccatccttcaaagatagtcatggagctatcattctgattggccaaaagagggttgagttt----------------------------------------------------

upper sequence: GLYMA04G40580.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv16s0098g00850.t01 (Vitis vinifera), 5'ss of exon 7
ACTGGAGCTGTAGTCAACATGATTGTCTCAAAGTATCCCACTATTAAGGGCATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaattgaatcatcatcatgtcaaatttagaggtcctgcttatattagatcacttaccattgtcaattagtcat---aagttgttatatgttggttaatattgtttgactaatggttacctaacatcaaaattggcattgatattttttattag
||||||||     | ||||||||  | || || || |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||| ||||  |        |||  ||||||   | | |||      |||| ||   |   |||   |   |  |  |    ||||    | | |  | | |  |||| |  ||                                                    
ACTGGAGCCACCCTTAACATGATCATATCCAAATACCCCACTATTAAGGGCATTAACTTTGACTTGCCTCATGTTATTGATGATGCCCCATCTTATCCTGgtacat--------atccacatcattctacaattaattcatctgcataccatccttcaaagatagtcatggagctatcattctgattggccaaaagagggttgagttt----------------------------------------------------
















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|192312639|gb|FK004327.1|FK004327
EST:     CATTAATTTTGATTTGCCC-ATGTCATTGAAGATGCCCCATCTTATC-AG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
EST: gi|58023205|gb|CX709946.1|CX709946
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|308098852|gb|HO760693.1|HO760693
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|6846392|gb|AW348682.1|AW348682
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|58024433|gb|CX711174.1|CX711174
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|308098520|gb|HO760261.1|HO760261
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|192312640|gb|FK004328.1|FK004328
EST:     CATTAATTTTGATTTGCCC-ATGTCATTGA-GATGCCC-ATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
EST: gi|151408242|gb|EV278050.1|EV278050
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
EST: gi|58014948|gb|CX701690.1|CX701690
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|21600756|gb|BQ611087.1|BQ611087
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|192325472|gb|FK017213.1|FK017213
EST:     CATTAATTTTGATTTGCCTCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|298196737|gb|HO041480.1|HO041480
EST:     CATTAATTTTGATTTGCCCCATGTCATCGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATGTGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|58016278|gb|CX703020.1|CX703020
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|31310859|gb|CD396062.1|CD396062
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|193358386|gb|FK324088.1|FK324088
EST:     TTTGATTTGCCCCATGTCATTGAAGATTGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: TTTGATTTGCCCCATGTCATTGAAGA-TGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|58019374|gb|CX706116.1|CX706116
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|151398983|gb|EV268854.1|EV268854
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTTCCAAAAGCTGATG
EST: gi|151407679|gb|EV277494.1|EV277494
EST:     CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAG                         GAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT
genomic: CATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaa ... tttttattagGAGTGGAACATGTTGGTGGAGATATGTTTGTCAGTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGAGCTGTAGTCAACATGATTGTCTCAAAGTATCCCACTATTAAGGGCATTAATTTTGATTTGCCCCATGTCATTGAAGATGCCCCATCTTATCCAGgtatcttaaattgaatcatcatcatgtcaaatttagaggtcctgcttatattagatcacttaccattgtcaattagtcataagttgttatatgttggttaatattgtttgactaatggttacctaacatcaaaattggcattgatattttttattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG