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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagggaagcctagaattttgtcatgcttcctttgataacaataaaccttgaatttccatgttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA

Basic information

species Glycine max
transcript GLYMA16G16060.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 3
-cagggaagcctagaattttgtcatgcttcc-tttgataacaataaaccttgaatttccatgttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
    |||  | ||| |  ||    | | |   |   ||   |        | || |    | |      |  |  ||   ||  ||  ||| |  | |  ||||       || ||  |   ||| || |||   || |||||||| ||||||||| ||||||| ||  | || |||||||| |||||||||||||| ||  
gataggatacttagtaactttctgtacctgtatcctattttagatctgtcttaactcatttctgccaggagcttctctgtttccttgacataa--tgcacagAAGATTAAGATGGGATTAGGAAATCTTGAGGCAACTTTTGAGACCTTGGTTGATGCATTTGTTTTTTTGGATAAGAACAAAGATGGATATGTCAGTAAGG

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G142693_T02 (Zea mays), 3'ss of exon 3
cagggaagcctagaatttt-gtcatgcttcct-ttgataacaataaaccttgaatttccatgttttgctacatcttcaaattgttt---tccatgac----ttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
          |||| | || | ||||| ||   |||||  |  ||      || ||    | || |   || | |  | |||| ||    || ||||    | || |||| |  | |||| ||| |    || || || |  |||||||| || ||||||||  ||||||| ||| | ||||||||||| |||||||||||||| || |
-------tgttagagtattagacatgcctcaagttgatttcc-tattttacgagttcttttattctatcac-tttggatattgcttgtgcccttgacattataccttagAGAAAAAGAATGGGGTTAGGGAACCTTGAACCAACATTTGAAACATTGGTTGAGTCATTTGTCTTCTTGGACAAGAACAAAGATGGATATGTCAGTAAGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G142693_T01 (Zea mays), 3'ss of exon 1
cagggaagcctagaattttgtca--tgcttcctttgataacaataaaccttgaatttccatgttttgctacatc-ttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
    ||| | | |  ||  ||||  ||  | ||| || || || |||  | ||  |  ||      |  | ||  | ||     |     |   | |     || | | |   |  ||  ||  | ||  |||   | |||||                                                            
-tttgaaacattgg-ttgagtcatttgtcttcttggacaagaacaaagatggatatgtcagtaagagtgagatgatacaggcaataaatgagaccattggagGAGAGCGCTCTTCAGGGCGCATAGGCATGAGA--AGATTTG------------------------------------------------------------

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G155822_T01 (Zea mays), 3'ss of exon 3
cagggaagcctagaat-tttgtcatgcttcctttgataacaataaaccttgaatttccatgttttgctacatcttcaaattgttttccatgac----ttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
      |   |||| | |||| ||||| ||   |    |   ||     ||  |||   |   || ||    ||    ||   | ||| ||||    |    |||| |  | |||| ||| |    |  || || |  |||||||| || ||||| ||  | ||||| ||| | ||||||||||| ||||||||||||||||| |
----ataagttagagtatttggcatgcctcgagttgagatcctattttatgtgttttttttaatt-ctgtccctctggatgtatgtccttgacatgatattttagAGAAAAAGAATGGGGTTAGGTAGCCTTGAACCAACATTTGAAACATTGGTCGAGTCTTTTGTCTTCTTGGACAAGAACAAAGATGGATATGTCAGCAAGA

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26470.1 (Arabidopsis thaliana), 3'ss of exon 3
--------cagggaagcctagaattttgtcatgcttcctttgataacaataaaccttgaatttccat--gttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
         |   |    ||    | |   |||||   |||||||    |     ||  ||||  ||  ||| | | |    || |||    |||   ||   |   |||||||    ||| || |||||||||||||| |  ||||| |||||  | ||||| |||||||| ||||||||| |||||||||| |||||||| |||    
gtacccgcaaaatacttttatcgatctcctatgctcggtttgata---tttcgttttagattttgattggttattcaatggttttaaagctatttttgtgtgatgaatagAAATGGACAATGGGAATGCCAAAGCTGGAACCAACATTCGAGACGCTTGTTGACACATTTGTGTTCCTAGACGAGAACAAGGACGGATATGTTAGCCGCG

upper sequence: GLYMA16G16060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01200.t01 (Vitis vinifera), 3'ss of exon 3
--cagggaagcctagaattttgtcatgcttcctttgataacaataaacct-tgaatttccatgttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
  |||       |    | |  |    |  ||    |  |  ||   | | || | |||  | ||    ||||| ||    |||| |||||||||    |||||||||||| || ||||||||||| ||||||   || ||||| ||  |||||||| ||||||| ||||| |||||||| |||||||| ||||| ||||| |
gccagttttcattttcctctcctggcacccccacccaacattatgtgcttatgtagttctttcttcccttacattttt---ttgtattccatgacactgctagAAATCACGGATGGGGATGCCAAATCTGGAGGCAACCTTTGAAACACTGGTTGATGCATTTGTGTTCCTGGACAAGAATAAGGATGGTTATGTGAGCAAGA

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|17964764|gb|BM271494.1|BM271494
EST:     GGATGACCCTGCAGCTCTTCACGCT                         AAATCACCACTTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTT
genomic: GGATGACCCTGCAGCTCTTCACGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTT
EST: gi|192311802|gb|FK003607.1|FK003607
EST:     TTCTTTGCGTTGTCTACCTTCTCAAGGATGACCCTGCAGCTCTTCACGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTT
genomic: TTCTTTGCGTTGTCTACCTTCTCAAGGATGACCCTGCAGCTCTTCACGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTT
EST: gi|192311803|gb|FK003608.1|FK003608
EST:     TTCTTTGCGTTGTCTACCTTCTCAAGGATGACCCTGCAGCTCTTCACGCT                         AAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTT
genomic: TTCTTTGCGTTGTCTACCTTCTCAAGGATGACCCTGCAGCTCTTCACGCTgtatcctagc ... acttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgaatttccatgttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA
                                      ttccatgac  putative branch site 
                                              cttccct  CT-rich tract
                              aaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagggaagcctagaattttgtcatgcttcctttgataacaataaaccttgaatttccatgttttgctacatcttcaaattgttttccatgacttccctagAAATCACGAATTGGGATGCCAAAGCTGGAGCGCACATTTGAGACTTTGGTTGATACATTTGTATTCCTAGACAAGAACAAGGATGGATATGTCAGCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - tcatgct
- - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctaca