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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttagttgtgattgctttgacttgacggacacaactacagaagtctataactcagattgcatgttagagtaataaaactttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG

Basic information

species Glycine max
transcript GLYMA09G33020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 2
cgttagttgtgattgctttgacttgacggacacaactacagaagtctataactcagattgcatgttagagtaataaaactttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
 || || | | | |    | || | |  ||     || |   | | | | |  | |||| | | |  |  |         || |      |||| || ||||||||||||| || |||||||||||||| ||||||||||| || |||
-gtaagatctaaat---ctaacctca-agagtttgctgcttcattgttttagcctgatttcttatacgtttt------tgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG

upper sequence: GLYMA09G33020.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 2
cgttagttgtgattgct--ttgacttgacggacacaact-acagaagtctataactcagattgcatgttagagtaataaaactttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
 ||| ||| |||    |  ||||||| |  | || |  | |  ||| | | |   |  |    ||| ||| |  |||     | |        ||||||||||||||||||||| ||||||||||||||||||||||| || || ||||||
tgttggttatgaaaaatgcttgacttca-agccatatttcatggaactatttgtataggccaacatattaaaaaaattg--ttgttgatcggtttggtttcagGATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG
















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|21602198|gb|BQ612529.1|BQ612529
EST:     GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAG                         GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
genomic: GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAGgtatgttgat ... ttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
EST: gi|192319502|gb|FK009484.1|FK009484
EST:     GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAG                         GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCC
genomic: GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAGgtatgttgat ... ttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCC
EST: gi|192311967|gb|FK004248.1|FK004248
EST:     GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAG                         GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
genomic: GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAGgtatgttgat ... ttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
EST: gi|192319503|gb|FK009485.1|FK009485
EST:     GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAG                         GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
genomic: GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAGgtatgttgat ... ttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
EST: gi|192311966|gb|FK004247.1|FK004247
EST:     GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAG                         GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
genomic: GTGATATGCTATTTACTCCCAAGGATGGACAAGGTTTTAGTGAGGATGAGgtatgttgat ... ttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataactcagattgcatgttagagtaataaaactttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
 ctataac  putative branch site (score: 3)
                   ttagagtaataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttagttgtgattgctttgacttgacggacacaactacagaagtctataactcagattgcatgttagagtaataaaactttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - -tgattgc
- - - - - - - - - tgacttg
- - - - - - - - - - - - - - -acacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc