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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactcattatgtttgatgtcagcttcttttatttcgtgtttcacaaatgagatctatgctaatttgtgttctttcttgaaaaaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATA

Basic information

species Glycine max
transcript GLYMA10G02410.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
gtaaactcattatgtttgatgtcagcttcttttatttcgtgtttcacaaatga-----gatctatgctaatttgtgttctttcttgaaaaaaat--tgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATA
      || |  | | |  | |     |   |   ||  || |  | || |||      |   ||  |||||    || | | |  ||| |  |  || ||||||||||| |||||||| ||||||  ||| ||||| |||||| | || |||||| | || ||||||||||||||||||||||||| ||| |||||| | 
-ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
















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|24205678|gb|BU964931.1|BU964931
EST:     TTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
genomic: TTATTAGGAGACTTCCACGAAGgtaaactcat ... aaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
EST: gi|23064134|gb|BU578907.1|BU578907
EST:     AGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
genomic: AGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcat ... aaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
EST: gi|208157183|gb|GD955869.1|GD955869
EST:     AATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
genomic: AATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcat ... aaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
EST: gi|33389718|gb|CA852925.1|CA852925
EST:     TCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
genomic: TCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcat ... aaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
EST: gi|58023725|gb|CX710466.1|CX710466
EST:     AATAGACTTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAG                         ATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT
genomic: AATAGACCTTTTGATCTTGATGAGGCTGTTATTAGGAGACTTCCACGAAGgtaaactcat ... aaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcacaaatgagatctatgctaatttgtgttctttcttgaaaaaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATA
                    tgctaat  putative branch site (score: 2)
                                   tttcttgaaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactcattatgtttgatgtcagcttcttttatttcgtgtttcacaaatgagatctatgctaatttgtgttctttcttgaaaaaaattgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA