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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG

Basic information

species Glycine max
transcript GLYMA19G35510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 1
taattgtttttg-tattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatg-tatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
   || |      || |  | ||    ||     ||  |    |     |  |||  ||   ||| | |  |    |  | | || ||      ||  ||||||||||||||| |||||  || | |||||||| ||||| || ||||| ||||| ||||| |||||||||||||||||||| || ||||| || || ||||
--cttataaccaatagttggctctactattaaacttgctcttatgctcttttttacttgtgagaagttttttataaccaaacttgataaatcatttcttcagGTTCTCTCTGTGGTTGGAATTTTGCAAGATGAGGTTGACCCTATGGTTTCTGTCATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCGGACATCGGTG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 1
--taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattag--atgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
  | ||| || || |  |   || ||| |         || || |  || ||  |||  ||  |     | ||       |  |||   |       ||  |||||||| ||||| || ||  || | ||||||||||||||||| ||||| ||||| ||||| || || || || ||  ||||||| |||||||| |||||||
tatcatt-ttcttatgatcgaataagtgactcaacc--gtaca-tccatgtggctagtaattttaatgctctagcaagcttgctcactaaatccctatttccagGTTCTGTCTGTGGTCGGAATTTTGCAAGATGAAGTTGATCCTATGGTTTCTGTGATGAAAGTGGAGAAAGCTCCGCTGGAATCCTATGCTGACATTGGTG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 1
--taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
  |  |   |      ||    | | |       ||| ||| | ||| | |||  |   |   ||  |  |     | |  |||   |    |     ||||||||||||||| |||||  |  | ||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| |||||||| |||||||
tgtgctcaataaccatttgttgtaaattgcacgctttagtgga-ttgttttgaccatcagg-agaggttcatcttgtttgctcactcaaatgttcacttcagGTTCTCTCTGTGGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCGCCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 1
-taattgtttttgtattaagatcagtcatctct---ttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
  |||   |  ||       |    |   ||||   |||| || | ||  |    ||  |||||      ||||  |  |||  |    ||| |||  |   ||||||| || || |||||  || | ||||| ||||||||||| ||||| ||||| ||||| |||||||||||||||||||| || |||||||| |||||||
aaaatcaatgctgctcctcaagtgatgtactctgtgttttatgtacttccttgatttgaatgcttatttagtaa-acagcttggc-caaatgtttccct--tagGTTCTGTCAGTGGTTGGTATTTTGCAAGACGAAGTTGATCCTATGGTTTCTGTGATGAAAGTTGAAAAGGCACCTTTGGAGTCTTATGCTGACATTGGTG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 1
-taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagat--gctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
 |  |||  || | |     || |||   |  |||       || |     |  |     ||| |   | | |  |      |||  | |  ||  |  ||||||||| ||||| |||||  |  | ||||||||||||||||| ||||| ||||| ||||| ||||| || |||||||||||||| |||||||| |||||||
tttgttgcatt-gcacatgcattagtggaccgtttacaactggtaggggatagcaagccagcttgttttctcactcaaacagtcaaatgt--ttactcttcagGTTCTTTCTGTAGTTGGTATATTGCAAGATGAAGTTGATCCTATGGTATCTGTGATGAAAGTTGAGAAAGCACCTTTGGAATCTTATGCTGACATTGGTG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 1
taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
           ||||| || |     ||    ||   || |   |   |||    || ||   | ||| ||  || |||| ||      || | |   |||| ||||||||||||||| |||||||||||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |
-----------gtattgagttttacaatgctcttccatggaaacgt--tgaaccaattcttcta-tgtgatattttttattat------ttttgtgatagGTACTCTCTGTTGTTGGGATTCTTCAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTGGAGAAGGCTCCTTTGGAGTCATATGCTGACATTGGAG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 1
taattgtttttgta-ttaagatcagtcatctctttttgtgcagttgatatgatta---gatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
     || | || | ||| | |     |    | ||| ||  ||   || ||||    | || ||   || ||  | | || ||      | ||| | | | |||||||||||||||||||| |||| ||||||||||| ||||||||||| ||||| ||||| ||||| || || |||||||| ||||||||||||||||| |
-----gtatgtgaaattagggtttaagaatcttgtttttgttgtgattacgattgtgtgttgttgtggatttagggttgctgat------ttgttttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCTGTGATGAAAGTTGAGAAAGCTCCTTTGGAGTCATATGCTGATATTGGAG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 1
taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagat-gctggaaatgt----aatgcttcttatcatgtatggttct---ttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
        | ||| |||   | |  |||   | ||      |  ||| |  ||   |  |    |  ||       | |||||||  |   | || ||   |  ||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| || || ||||| ||||| ||||| || ||||||||||||||||| || || |
--------tctgttttatagttatgcattcttattcacattgaagatgtagttccttcaccatcatagtttcaggaggttcttatattactttgtgctgtctcgtcagGTTCTTTCTGTTGTTGGTCTTCTCCAAGACGAAGTTGATCCAATGGTGTCCGTAATGAAAGTTGAGAAGGCTCCATTGGAATCATATGCTGACATAGGAG

upper sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 1
---taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
   | |  ||   || ||||      |   || |       |     | ||| |  ||||  ||| ||  |  | |     ||  | | ||  ||||   ||||| || || ||||| ||  | || |||||||| || || |||||||| ||||||||||| |||||||| || ||| | || ||||||||||| |||||||
aagttagagtaactg-attagtcctggcggtcacgaacatggtttgagttatcaccagatcatgggaaacttgtccaaacgattttctttg--tcttgtgcagGTCCTTTCAGTTGTGGGATTGCTGCAAGATGACGTGGACCCAATGGTTTCTGTTATGAAAGTTGAAAAAGCTCCTCTAGAGTCATATGCTGACATTGGTG

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|254326967|gb|GR836576.1|GR836576
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|22541543|gb|BU091386.1|BU091386
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|209716528|gb|BW676952.1|BW676952
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|24135970|gb|BU926480.1|BU926480
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGCTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|209699123|gb|BW656163.1|BW656163
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|308099190|gb|HO761031.1|HO761031
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|308098232|gb|HO759973.1|HO759973
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|26045684|gb|CA783191.1|CA783191
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAAAAAG                         GTTCTCTCTGGTGTTGGGCTTCTTCAAGATGAA
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAA
EST: gi|20815126|gb|BQ299604.1|BQ299604
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGCTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|20814952|gb|BQ299430.1|BQ299430
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
EST: gi|24135978|gb|BU926488.1|BU926488
EST:     TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAG                         GTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT
genomic: TCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttag ... tctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG
 agttgat  putative branch site (score: 5)
                                            ttctttatc  putative PPT
                 aaatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattgtttttgtattaagatcagtcatctctttttgtgcagttgatatgattagatgctggaaatgtaatgcttcttatcatgtatggttctttatcagGTTCTCTCTGTTGTTGGGCTTCTTCAAGATGAAGTTGATCCAATGGTCTCTGTTATGAAGGTTGAAAAGGCACCTTTGGAATCATATGCTGATATTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - gcagttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgg