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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttccgttttcgcttacttattactgcctccgttcctaaacataaggctcttttaacactcgtgctgtttcgcatgctccgttatgatataattgaatggtcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT

Basic information

species Glycine max
transcript GLYMA07G30080.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G30080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0017g00540.t01 (Vitis vinifera), 3'ss of exon 2
gttttccgttttcgcttacttattactgcctccgttcctaaacataaggctcttttaacactcgtgctgtttcgcatgctccgttatgatataattgaatggtcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
  ||||   | | ||  | |||| | | | |  |||  |     |     | || |||   || ||     || |||  || | |   | ||  | ||        || ||| | |||||||||||||||| |||||| ||||||||||| ||
--tttctaatct-gcaaagttataa-tacttatgttattgt---tgtcattgttataaggttcttgg----tcacataatctgattctaaatt-tcgatcaacatgttgcagATGTTGGAGTATTGGGCTGGCAGGGGAATGCTGCAGATTTT
















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|192319319|gb|FK009861.1|FK009861
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|192319318|gb|FK009860.1|FK009860
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|31458341|gb|CD400369.1|CD400369
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|9258019|gb|BE346142.1|BE346142
EST:     GCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: GCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|7028830|gb|AW458613.1|AW458613
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|58022562|gb|CX709303.1|CX709303
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|6845786|gb|AW348076.1|AW348076
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
EST: gi|58022278|gb|CX709019.1|CX709019
EST:     TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAG                         GTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
genomic: TCGTGGTCCTCGCCGAGACCGAATGGAGCTTCATCTTAAAGTTCTCCAAGgttttccgtt ... tcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactcgtgctgtttcgcatgctccgttatgatataattgaatggtcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT
 ttttaac  putative branch site (score: 2)
                                             tcctttac  putative PPT
                          ttatgatataattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttccgttttcgcttacttattactgcctccgttcctaaacataaggctcttttaacactcgtgctgtttcgcatgctccgttatgatataattgaatggtcctttacagGTTTTGGAGTATTGGGCTGCCAGGGGTATGCTGCAGATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT