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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

Basic information

species Glycine max
transcript GLYMA10G02400.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
gttggtagattttctttttagttgctttaa--atgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
          | | ||||  |  |  |  |  || | | || |   || |  |||  |  ||   | || |||| |     | ||  ||    |||| |   ||   |  |||||||||||||||||||||| ||||| || ||||| || || ||||| |||||||| ||||| |||||||||||||| || || || ||||||||||| |
---------ctatattttgggacggatggagtattatatgttggctacctaattttctctatttaagtcctatcttaaaaattgcctctg---gtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 21
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatat---agCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
|||   |     |     || |   |||  ||    |||||||    ||||||| |   |    || || | ||  ||| |    ||  |||| ||| |||  | | |   |||| || || |||||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| || || || ||||| || |||||||| || || |
gttatgaatggatgggggtactacttttggat----agtggaa----ttttttatt---tccattttatttgata-gtgaactgactt-ttgttattgcttatgttgtgccagCCATGTAAAGGAATATTACTTTTTGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
gttggtagatt--ttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
  | | |   |  || |  |    || |||   |     ||        | ||||      |   | |  | |||      |||   || ||    |||  ||       |||| || |||||||||||||||||||| || ||||| || || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
--tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctttt------ttccacttgtttcacaaacatagt-tctgatcaccatttattcac---cagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
    |||   ||   | |     | ||||||     |   | | |  || || |     |    |  | ||| | |   |  | || || |  | |  |||||     ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||||||| || || |||||||| || || |
----gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
gttggtagattt-tctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
 || ||| |||  |  | |||| |   ||    |     | ||| || |   || |||||| || || || |  | ||   |  | | |    | ||| |||||     ||||||||||||||||||||||||| || || |||||||| || ||||| |||||||| || || |||||||||||||| || || |||||||| || || |
-tttgtatattagtagtgttagatatgttgggcgt----ttgaaaacttcaatt-gtagattattttgatgtactatggtcatgatccccaatttatt-ctttg----cagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 1
gttggtagattttc-tttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
     ||   ||   | | |    | ||||||     |   | | |  || || |     |    |  | ||| | |   |  | ||||| |  | |  |||||     ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||||||| || || |||||||| || || |
-----taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagat-gatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
  | | |   ||  | |||  |     |||   |  | |||||||||  ||||||  ||  || |   |  | ||||   |   |    ||| ||  |||         |||| || || ||||| || |||||||| || ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| ||||| |
-atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattcta--tacc--------agCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
gttggtagattttc-tttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
     ||   ||   | | |    | ||||||     |   | | |  || || |     |    |  | ||| | |   |  | ||||| |  | |  |||||     ||||||||||||| ||||||||||| ||  | |||||||| |||||||| |||||||| || || ||||||||| |||  || || |||||||| || || |
-----taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
gttggtagattttctttttagttgctttaaa--tgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
  || |  ||| ||    ||   |  |       ||| ||| |      | ||  |  ||  ||  || | |||||  ||       || ||  |   || ||  |    |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
agtgattaattgtccgagtaaccgactaggggtcgactagtcgcctg-gtcttcgaccaggcgac-ttgaaatcattggt------tctgatcat--ctattt--gccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
                    ||  |||| | ||  |   |||     || |||  ||| || || || || |||   || | |    |||     | |  ||  ||  |||||   || || ||| || | ||||| || ||||| || ||||| || ||||| ||||| || ||||||||||| ||||| ||||||||||| || || |
--------------------gtaccttttattgctatacggat----ttatttgttagttgttactccta-cataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
--------------------------------------gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtag-atgatattcatatcatgtgtgt--agcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
                                      ||   || || |  | | ||  || |  || |  |   || |  |      | |||   ||   ||||||  | ||| |||  | || || | ||   ||||| |   |  ||||||||||||||||  | || |||||||| ||||| || ||||||||||||||||| ||||| || |||||||| || || |||||||| || ||||| |
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactattt-ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

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|16279552|gb|BI943495.1|BI943495
EST:     TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAG                         CCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAGgttggtagat ... ttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
EST: gi|192316675|gb|FK009360.1|FK009360
EST:     TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAG                         CCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAGgttggtagat ... ttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
EST: gi|37994806|gb|CF806395.1|CF806395
EST:     TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAG                         CCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAGgttggtagat ... ttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
EST: gi|207817720|gb|GD792677.1|GD792677
EST:     TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAG                         CCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAGgttggtagat ... ttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT
                                        ttacttt  CT-rich tract
                                 attgtaattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA