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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA

Basic information

species Glycine max
transcript GLYMA05G35000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
taacttatcattgattgtgttcatcttttgttgtaactttttttttt-taaattt-gtaattggcacctatc---ttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
  | |  |  |||    |      ||  ||  ||| ||   |       |||| | ||||||  ||  |||    || |  |   |  |  ||  || | || |||||| || ||||| ||| |  | |||||||||||| ||||||||||||| ||||| ||||| || || |||||||||||||||||||||||||| || ||
--attcttttttgggatttcaagcctcatga-gtagctgcatacagaacaaatctagtaatt--catttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacctatcttg-tcaaactttttttgtctatgtat---gtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
    || |     |      |    ||   || | | |   | || |  |  ||||   ||  |   || | | ||| || || ||      ||| |   | |||||| || ||||| ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| ||||||||||||||||| || ||
--ttttgttcacaagaacaatggatttgaattctgaatacctgttatgcatgttgtg--tgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 1
taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacctatcttg-tcaaactttttt---tgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
    || |     |      | |  ||    | | | | | |  | || |  |||   |||  |   || | | ||| ||||| ||   || |  | | || |||||| || ||||| ||  |  | ||||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| ||||| ||||||||||| || | 
--ttttgttcacaagcacaatgaatttgaactctgaatatctgctattcatgttgc--ttgataataatttagatcatactttgttctatggcgttttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATT

upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------------------------taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacc-tatc-ttgtcaaactttt-----tttg------tctatgta---tgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
                                                            |      | |||| ||   |   | |   ||    | |||  ||    | |||   || |  | |  |||| ||||  | | |||     ||||      | | |||    || |||||| || ||||| ||||||||||||||||| || ||||||||||| |||||||||||||| || || || |||||||||||||||||||||||||| | 
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttgttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT

upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaat--ttgtaattggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
 ||  |           || ||    || | | ||  | |  | | | ||||  ||  | ||||   | || ||   ||    ||  | | | || |||||||||| |||||||| ||||| |||||||||||||| ||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| ||
gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgat-tttgtg-atgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1
taacttatcattgattgtgttcatctt-ttgttgtaactttttttttttaa-atttgtaat--tggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
    ||||| | ||   | |||   || ||||||  || |  | |||| |    ||| |    | |||       | ||    |  ||||||     |||| |||||| ||||| ||||||||| ||||||||||||||||||| || ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||
----ttatcttggaaaattttctggttgttgttgctacatggtcttttgagtgcttgcatgcatagcaggagatatatctttgtgattttgtggtcatatgcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA

upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S311_60V6.1 (Physcomitrella patens), 3'ss of exon 1
--taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
   |||||  ||    ||| ||  |  || |  |  ||||  |   |||     ||||      |     || |  |     |  | | |   | | || |||||| ||| ||||  |  |  | ||||| |||||||| |||||||| ||||||||||| || |||||||| ||||| ||||| || | ||| ||| | | 
tccaactttccacaatttgagt--agtttcttctagaactgctgcatttgcgtgttgtgtgattccttagtcctacccttgatagtgtattgttatctgcagTTCCAAGGGACTTTCGTCTTCTTGAAGAACTTGAGAGGGGTGAGAAAGGAATTGGAGACGGGACTGTTAGTTATGGCATGGACGACGGTGACGATGTGTT

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|6069685|gb|AW099309.1|AW099309
EST:     CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|254342628|gb|GR858790.1|GR858790
EST:     AATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: AATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|192319728|gb|FK011866.1|FK011866
EST:     CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|21889833|gb|BQ743046.1|BQ743046
EST:     CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAACTTCAGATTATTGGAAGAGCTTTGAGAGAGGTGAGAAGGGA
genomic: CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGC-TTGAGAGAGGTGAGAAGGGA
EST: gi|24135406|gb|BU925916.1|BU925916
EST:     CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCG                         TTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CAATTCCAATTCACCCTCAAACATGGGTTCTGAAGGTTCCACTGTCGTCGgtcagtattc ... atgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatttgtaattggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA
                                 ctttttttgtctat  CT-rich tract
                              aaacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacttatcattgattgtgttcatcttttgttgtaactttttttttttaaatttgtaattggcacctatcttgtcaaactttttttgtctatgtatgtagTTCCTAGGAACTTCAGATTATTGGAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - -tgtgttc
- - - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtca