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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttccttcatatatcctgtaggtttgccagcgttagccttaatataaactgtacattttcagagtaaaattttgattcttttctgcccttggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCAATGGATATCAGTGGCGAGCAGCATCTTGACATA

Basic information

species Glycine max
transcript GLYMA08G07840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0178g00020.t01 (Vitis vinifera), 3'ss of exon 2
gttccttcatat-atcctgtaggtttgccagcgttagccttaatataaactgtacatt--ttcagagtaaaatt-ttgattcttttctgcccttggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCAATGGATATCAGTGGCGAGCAGCATCTTGACATA
  |     |||| | | |||    ||||  |  | |   ||| | | ||   | || |  ||||  ||    |  |   |  |  | |    ||| || ||||||||||||| ||||||||||| ||||  |||||  |||||| | | ||||| |||||||| ||||| || ||||||| ||| |||
--tgtaaaatattaacttgtgaaattgc--gtttaatttttagtttgaatattccactaattcatggtttgttggtccgtgttcctttttgtttgaaagtgcagTTTGATGTGACTTTTCCTGCCGTTCCTTGTTCGGTACTCACTCTTGATGCCATGGATATTAGTGGAGAACAGCATCATGATATA

upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S72_188V6.2 (Physcomitrella patens), 3'ss of exon 3
-----gttcc---ttcatatatcctgtaggtttgccagcgttagccttaatataaactgtacattttcagagtaaaattttgattcttttctgcccttggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCAATGGATATCAGTGGCGAGCAGCATCTTGACATA
      |||    |  ||||   | |   ||      || |||    ||| |  ||| | | | | | |  |||  |  |||  |  ||| ||   ||       ||||| ||  |||| || || ||  |    ||||| ||  |||| ||||||||||||||||| ||||| |||||||| ||  |  | 
cctgaattcaagatagatatgctccgagtgtgcatgggctttaagactaa-acgaacagcagagtcttat-gtatcaagttgtgtgatttatgttttta------cagTTGGACATCACGTTCCCAGCATTGGCGTGTTCTATGGTCAGCTTAGATGCAATGGATATAAGTGGTGAGCAGCACCTCAATGTG
















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|208276377|gb|GE076939.1|GE076939
EST:     AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT                         TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... ggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGA
EST: gi|209704674|gb|BW675882.1|BW675882
EST:     AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT                         TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... ggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
EST: gi|298191603|gb|HO039082.1|HO039082
EST:     AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT                         TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... ggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
EST: gi|192299471|gb|FG988755.1|FG988755
EST:     AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT                         TTTGATGTCACTTTTTCCTGCTGTTCGATGTTTCAATACTCAGTTTTAGAT
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... ggaaatgcagTTTGATGTCACTTTT-CCTGCTGTTCGATGTT-CAATACTCAGTTT-AGAT
EST: gi|192326043|gb|FK016915.1|FK016915
EST:     AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT                         TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... ggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
EST: gi|193632629|gb|FK580533.1|FK580533
EST:     AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT                         TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... ggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgtacattttcagagtaaaattttgattcttttctgcccttggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCAATGGATATCAGTGGCGAGCAGCATCTTGACATA
                        ttttgat  putative branch site (score: 4)
                              ttcttttctgcccttg  CT-rich tract
                   taaaattttgattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccttcatatatcctgtaggtttgccagcgttagccttaatataaactgtacattttcagagtaaaattttgattcttttctgcccttggaaatgcagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCAATGGATATCAGTGGCGAGCAGCATCTTGACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- tccttca
- - - - - - -tcctgta
- - - - - - - - - - - - tgccagc
- - - - - - - - - - - - - - - - - -gccttaa
- - - - - - - - - - - - - - - - - - - - - - - -actgtac