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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaatgtacaaaatagttaatttagcagatgagtgaatttttaatctattaacagactttgaacttgaatgttccttcaactaagaggattgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGATGATTCAACACGAGTTGTTACATCTG

Basic information

species Glycine max
transcript GLYMA16G27960.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27960.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G001904_T01 (Zea mays), 3'ss of exon 1
-gtaatgtacaaaatagttaatttagcagatgagtgaatttttaatctattaacagactttgaacttgaatgttccttcaactaagaggattgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGATGATTCAACACGAGTTGTTACATCTG
 ||   || ||| |  | |  |  |   ||  |||    || |||   | | | || |||   | |  |         |   |       || || | |||||||||||||| || |||||||| |||||  | || |||||||| || |||||||||||     | || ||  |||
tgttgagt-caacactgcttttaaaatggaaaagtatgcttataacaaaattaaagtcttcttattccacatccataactgtttgtgaacttcaacttcagGGATTTGCAGAGCTGGAATATGGAATGCTTCGCTATATGGGAGCTATAGATGATTCAACCATGATAGTAACTACTG

upper sequence: GLYMA16G27960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G76730.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgtacaaaatagttaatttagcagatgagtgaatttttaatctattaacagactttgaacttgaatgttccttcaactaagaggattgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGATGATTCAACACGAGTTGTTACATCTG
|| |  |     | | || ||||   |  |     |  | ||| |  |  | || ||  |    ||| |  ||  |   |||| | |        ||||||| ||||| ||||| |||||||| ||| || | |||||||||||||| |||||||| ||||  ||||||||| |||
gtgagatttgttacaattcattt--taactttaaaagatattagttga--accaaaccatatgattggagtttgatatgactatgtg--------tgcagGGTTTTGCGGAACTCGAATATGGAATGTTGCGTTACATGGGAGCCATTGATGATTCCACACCCGTTGTTACAACTG

upper sequence: GLYMA16G27960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 3
------gtaatgtacaaaatagttaatttagcagatgagtgaatttttaatctattaacagactttgaacttgaatgttccttcaactaagaggattgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGATGATTCAACACGAGTTGTTACATCTG
       | |  |  |     |||  |   ||   | ||     ||| | | ||    | |  ||| |    |||| | |    |  |   | |  |    | ||||| |||||||||||||||||||| ||| || |||||||||||||||| |||||  | || |   |||| || || |
actatcttgacatctacttgtgttgttactgcttcttagaatggtttcactttacc--ctgtttttaa----gaatttactggaatttgtcatgtctctgcttcagGGGTTTGCAGAACTTGAATATGGGATGTTGCGGTACATGGGAGCCATAGATGACACTACTCCTATTGTCACCTCAG

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|22525267|gb|BU084078.1|BU084078
EST:     GATCTGTTGCTGTTGATCCAAAGACAGGTGCTCGATTGGGAAAGGGAGAG                         GGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGAT
genomic: GATCTGTTGCTGTTGATCCAAAGACAGGTGCTCGATTGGGAAAGGGAGAGgtaaagttgg ... tgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGAT
EST: gi|51338397|gb|CO982263.1|CO982263
EST:     GATCTGTTGCTGTTGATCCAAAGACAGGTGCTCGATTGGGAAAGGGAGAG                         GGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGAT
genomic: GATCTGTTGCTGTTGATCCAAAGACAGGTGCTCGATTGGGAAAGGGAGAGgtaaagttgg ... tgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattaacagactttgaacttgaatgttccttcaactaagaggattgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGATGATTCAACACGAGTTGTTACATCTG
 tattaac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtacaaaatagttaatttagcagatgagtgaatttttaatctattaacagactttgaacttgaatgttccttcaactaagaggattgaagtgcagGGATTTGCAGAACTTGAATATGGTATGCTGAGGTACATGGGAGCCATCGATGATTCAACACGAGTTGTTACATCTG

- aatgtac
- - - - - - - - - - - - gcagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gactttg