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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatcactgattgtgttcatcttttattgtaacttcttttttttttgtaaatttgtaatttgcacctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA

Basic information

species Glycine max
transcript GLYMA08G04710.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
cttatcactgattgtg--ttcatcttttattgtaacttcttttttttttgtaaattt-gtaatttgc--acctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
   ||   |  ||| |  ||||    | ||   |    ||   |       |||| | ||||||     |   |  |  |||   |  |  ||  || |  |||||||| || || || ||| |  | |||||||||||| ||||||||||||| ||||| ||||| || || ||||| |||||||||||||||||||| || ||
---attcttttttgggatttcaagcctcatg--agtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
-cttatcactgattgtgttcatcttttattgtaacttctttttttt----ttgtaaatttgtaatttgcacc-tatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
  || |     |      |    ||  ||| | | | | | || |     ||||    |  ||||||  | | || ||||||      | |||| | | |  |||||||| || || || ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| ||||| || ||||||||||||||||| || ||
ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgtt-----ctatggtgtct-tctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 1
-cttatcactgattgtgttcatcttttattgt-aacttcttttttttttgtaaatttgtaatttgcacctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
  || |     |      | |  ||  | | | ||  |||  | ||  |||   ||  ||||        ||| |  |    | | |||  | | |  |||||||| || || || ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| ||||| || ||||| ||||||||||| || | 
ttttgttcacaagcacaatgaatttgaactctgaatatctgctattcatgttgcttgataata-atttagatcatactttgttctatggcgttt-tctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATT

upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------cttatcactgattgtgttcatct-tttattgtaacttcttttttttttgtaaatttgtaatttgcacc-tatc-ttgttaaa-------atttttggtctat--------gttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
                                                            || |   | ||||  | | |   ||||  |||||   ||||  ||    | |||   || |  | |  |||| ||||| |        || |||| |  ||        ||| |||||||| || || || ||||||||||||||||| || ||||||||||| |||||||||||||| || || || || ||||||||||||||||||||||| | 
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacga-ttttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT

upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
cttatcactgattgtgttcatcttttattgtaact-tcttttttttttgtaaatt--tgtaatttgcac-ctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
        |||| |  | |||  | |    ||  | | | | |  | |||||| |  | | |||||    | || ||  ||| |  ||   | | || | | |||||| ||||| || ||||| |||||||||||||| ||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||||||||| ||
---gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtgat-gtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1
cttatcactgattgtgttcatcttttattgtaacttcttttttttttgtaaatttgta-----atttgcacctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
 |||||   ||   | |||     || ||||  || | |  | |||||     ||| |     |   | |  ||| |  ||   |||||  |   || |  |||||||| ||||||||||||||| ||||||||||||||||||| || ||||||||||| ||||||||||| || || ||||||||||||||||||||||| ||
-ttatcttggaaaattttc--tggttgttgttgctacatggtcttttgagtgcttgcatgcatagcaggagatatatctttgtgattttgtggtcatat--gcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA

upper sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S311_60V6.1 (Physcomitrella patens), 3'ss of exon 1
-----cttatcactgattgtgttcatcttttattgtaacttcttttttttt-tgtaaatttgtaatttgcacctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
     |||  |||   ||| ||  |  || |  |  |||| ||   |||   |||    |  |   ||   |||| | | | | | | | | ||   | |  |||||||| ||| | ||  |  |  | ||||| |||||||| |||||||| ||||||||||| || |||||||| || || ||||| || | ||| ||| | | 
tccaactttccacaatttgagt--agtttcttctagaactgctgcatttgcgtgttgtgtgattccttagtcctaccct-tgatagtgtattgt---tatctgcagTTCCAAGGGACTTTCGTCTTCTTGAAGAACTTGAGAGGGGTGAGAAAGGAATTGGAGACGGGACTGTTAGTTATGGCATGGACGACGGTGACGATGTGTT

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|18041432|gb|BM309726.1|BM309726
EST:     CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|192319053|gb|FK010617.1|FK010617
EST:     CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|18716865|gb|BM522906.1|BM522906
EST:     CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|298190494|gb|HO032615.1|HO032615
EST:     CAATTCCAATTCGTCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTATGAATTTCAGATTATTAGAAGAGCTTGAGAGAGGTGAGAATGGAA
genomic: CAATTCCAATTCATCCTCTAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaaatttgtaatttgcacctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA
                      tatcttgttaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatcactgattgtgttcatcttttattgtaacttcttttttttttgtaaatttgtaatttgcacctatcttgttaaaatttttggtctatgttcgcagTTCCTAGGAATTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacct