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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

Basic information

species Glycine max
transcript GLYMA19G41840.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
||| |||  || | ||     |   |  | ||| |     | |   |  ||        |||| ||||| ||    |||   ||||| ||||||||||||||||||||||| || || || |||||| | || || ||||||||||| || || |||||||| ||||| ||||| |||||||| |
gtaaatgctca-atatcttttttggataaatacttcaaaattcag-gaaat--------tttaattatgcttc--cttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttactt--atggtttattttctat-cagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
               || | ||  |||  ||  |||| | |    |  |  | ||||       ||  ||  |  ||  |  || |||||  |||||||||||||||| ||||| || || || || ||| | || || |||||||||||||| ||||||||||| || || ||||| |||||||| |
--------------gta-atgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
------gtacatgtccagagatacaagtacaacc----------attacattccgttccgctgctatgttttctgt-ttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
         || |||   |||| |   || || |          |||| ||    ||  |  |  |        |  ||| | |||  |    ||||  ||||| |||||||||||||||||||| || || || || || ||| | || || ||||||||||| || ||||||||||| || || ||||| |||||||| |
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatc--cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
    ||||| | | ||   |||    |   | |||    ||  ||   |    |   |    | | ||| |   ||   |   |||||||||||||||||||| |||| |||||||| || ||||| || || ||||| |||||||| || |||||||||||||| || ||||||||||| || |
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagca-tgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
---------------gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
                  ||| |      ||  ||  |  ||  |     |       |    |     |||||     |        ||| |   |||||| ||||| ||||||||||| ||||| || ||  |||| ||||| || ||||| || ||||| ||||||||||| ||||| || ||||||||||||||||
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
                                       | |   |  |   || |         || |   |         ||||| |||||| ||||||||||||| || || ||  | || || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||
------------------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|7232737|gb|AW568091.1|AW568091
EST:     TGACATTCAAG                         GTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTC
genomic: TGACATTCAAGgtacatgtcc ... tttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
                                        tttattttct  CT-rich tract
                                  ttatggtttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT