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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG

Basic information

species Glycine max
transcript GLYMA10G10040.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g06020.1 (Oryza sativa), 3'ss of exon 4
--------------gtaataca--ctcttcattattgtcaaaaatt--tattagaacttgtt-tgcaatcctggttatgatattggtc-----atgctaacaacga-atattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
              | | |  |   | || | | |  | |   |||  | || ||  ||  |  |   || |  |  |   |||||       ||  |   ||    || |||||       |||||||| || |||||||| ||||| || ||  |||| |||||||| ||||||||||| |||||| |||||||||  || || || ||       ||    |
gtcagaattaagatggagtttaatttttttactgtgttgattgattggtttttgattttactgcgtgttcttcttggttgaattgggtgttgaattttgtgaattttattttggtttgatttcagGTTTCGAACTGGTTCATCAATGCCAGGGTGAGGCTGTGGAAGCCGATGGTGGAGGAGATGTACCTGGAGGAGACCAAGGACCAGGACGGCGGCGGCGGCG

upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G458728_T07 (Zea mays), 3'ss of exon 4
---------gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctgg-ttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
         |   |  |   ||| || ||    |   |       || |||  ||   | |||| || | | |||     | |  | ||  | | ||  |    |   |||| || ||||||||||| ||||| || || ||||| |||||||| ||||||||||| |||||| |||||||||  || || || ||       ||    |
gtcggtaaagctgtgaatctttctttctttcttatcctgcgaatcaatttgactgttttactggcttcttaaattaac--ttccgaaaaaaattgttcctttctgt-tagGTGTCCAATTGGTTCATCAATGCGAGGGTGCGGCTGTGGAAGCCTATGGTGGAGGAGATGTACCTGGAGGAGACAAAGGACCAGGACGCTGGAGGCGGCG

upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaatacactcttcattattgtcaaaaatttattagaacttgt-ttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATG--AACTAAATGGTTCTG
               |   | ||||||  | |||    ||||| ||   |   |  ||| || |  | |  |    | |   | | |   ||||     |||| || || ||||| || || || ||||||||| | ||||| |||||||||||||| |||||| ||||||| ||||| ||||| |  ||  | ||||     
--------------gtacgtttcaaaa--tgattctttcttgtgttattaggttacttaagaaagcgtttttaagtaaatttattttctttaattatttagGTGTCGAACTGGTTTATAAACGCGAGAGTTCGGTTATGGAAACCAATGGTGGAGGAGATGTACATGGAGGAAATGAAGGAGCAGGCAAAGAACATGGGAT--

upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 11
gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
    | | | ||  | | |||       ||| |  |   |||||||||     | |||||  |    |||       | |  |  || || ||    ||||| || || |||||||| |||||| | ||||| || ||||||||||||||||| ||||||||| |||||||  | || || || |||   ||||| || |
---gtgcgcgctagaatcttg----ggttttttgtgtctttgtttgca-----gattatgggaactctca-------accagagctttgtgataatgcagGTGTCTAACTGGTTCATAAATGCTCGGGTTCGTCTCTGGAAGCCAATGGTGGAAGAAATGTACATGGAGGAAGTCAAGGACCACGAAGAGAATGGATCAG

upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatacactcttcattattgtcaaaaatttattagaac--ttgtttgcaatcctggttatgatat-tggtcatgcta-acaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
        | || ||  |   |  || | | |  ||| |  |  |  |  | |         |||| ||    | | |      |   | | | |   || |||||||| ||||||||||| || ||  |||| ||||| |||||||||||||| ||||| |||||| | |||||    |||||| |      | ||  | |||
----cctccactccagaacgcttgaacagtgagaagatcagtcatcaggtagcagaaaatgaatatctgaatctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG

upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaa-cagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
  | ||  |    |  | |||| ||| ||  | |       |   |  ||     |  |   |   | | ||  |        |        || || ||||| || || |||||||| || ||  |||||||  | |||||||||||||| |||||||||||| |||||||   ||||||| |      | ||  |||| 
ccagtatccagaacgcttttgttaaacatccacttttgtcagaggg-gatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA

upper sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24138 (Selaginella moellendorffii), 3'ss of exon 6
gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG-
                            |   ||| ||   | ||     |  ||  | | |  | ||  ||     |||      ||| |      ||||| || || ||||| ||||||||  |||| ||||| |||||||| ||||| |||||||||||   ||||||||| |||||||| || ||    |||   | 
-----------------------gtgcgtgctttaaaaaaagcttttgtcctcgg--aagcttcttgttgtggct-taacttgctgtggaatctctgcagGTCTCCAACTGGTTTATTAATGCCCGAGTCCGGCTCTGGAAGCCTATGGTCGAGGAAATGTATCAGGAGGAGATTAAAGAGCAGGAGCTCGG-GGTGGCGT

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|308098270|gb|HO760011.1|HO760011
EST:     ACTCAGACAAGCACATGCTTGCTAAACAAACAGGGCTTACCAGGAGCCAG                         GTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTG
genomic: ACTCAGACAAGCACATGCTTGCTAAACAAACAGGGCTTACCAGGAGCCAGgtaacaccac ... aatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTG
EST: gi|23057384|gb|BU578058.1|BU578058
EST:     ACTCAGACAAGCACATGCTTGCTAAACAAACAGGGCTTACCAGGAGCCAG                         GTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTG
genomic: ACTCAGACAAGCACATGCTTGCTAAACAAACAGGGCTTACCAGGAGCCAGgtaacaccac ... aatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG
                         tgctaac  putative branch site (score: 1)
          ttatgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacactcttcattattgtcaaaaatttattagaacttgtttgcaatcctggttatgatattggtcatgctaacaacgaatattggtaatggaacagGTTTCAAATTGGTTCATTAATGCTAGAGTTCGGCTTTGGAAGCCAATGGTGGAGGAAATGTACTTGGAGGAGATGAAAGAGCATGAACTAAATGGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - tacactc
- - - - - - - - - - - - - - - - - - - - - - tgcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct