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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgactactgttattacaacttcttgcatgtgatcaacttgtggcttttatacactatgttgagtcctatttcattgactaaatgaaaacatcgtcgattttacagtattgtaatattgactgtcttgttcttaaatgatatcttgtgtctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG

Basic information

species Glycine max
transcript GLYMA14G13480.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 10
gtaattgactactgttattacaacttcttgcatgtgatcaacttgtggcttttatacactatgttgagtcctatttcattgactaaatgaaaacatcgtcgattttacagtattgtaatattgactgtcttgttcttaaatgatatcttgtgtctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG
          ||   |  |  || || |  ||  | | ||  |     ||| |||  |||  ||    ||    |  ||    | | || |||||  |    |   ||| ||   |||            | ||||||| |    || | ||| | |   |||||||| || |||||  |||| |||||| ||||||||||||||||||| || |||||  |||| ||||||||  |||||||||| || ||||| || || |
-------gtgacatatgctttaaattttcacagataa-cacttccattcttctatcgactg-gtgatttctccatatataatgtgactgcaaacactgcaattcacacaatacactaag-----------tattcttaatttgattcgtttgtatttg--cagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGAATTTCGTTGGCTGGATTGTCCCTGGCTAAATGCGAGTACCTAGCTGACG

upper sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S540_7V6.2 (Physcomitrella patens), 3'ss of exon 10
gtaattgactactgttattacaacttcttgcatgtgatcaacttgtg-gcttttatacactatgttgagtcctatttcattga-----ctaaatgaaaacatcgtcg--------------attttacagtattgtaat-attgactgtcttgttcttaaa--------------tgatatcttgtgtctctcat--cagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG
||| |||  || |   ||  |  |   |||| || | || |  |      |||  |||    ||  |     ||||  |||||     ||  |  ||  ||  |  |              |||  |  ||||| |  | |   ||  || | || | | |              || || | | ||| | |  |  ||||||||||| |||||  |||| |||||||| |||||||| ||||||||  | ||||| || || ||| |    ||||| || ||||  ||| | || ||||
gtatttg--tattaccatctcttcgatttgcgtgggctccaggtccacattttcgtacttgttgacgcagtttattctattgaaacctctttacaaagccactggtgcccacggttatcttattcgaaggtattttggttagctacattcgttttgtgagacgtacgtttacttctgctaacgtttgtttgtggtggcagAGTGACAATATGACTGACAAATGGCACGTGTACATGACCAAGGATGGTCGTATTTCACTTGCTGGACTCAACTTGGCAAAGTGTGCTTACTTGGCCGATG

upper sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ26197 (Selaginella moellendorffii), 3'ss of exon 8
gtaattgactactgttattacaacttcttgcatgtgatcaacttgtggcttttatacactatgttgagtcctatttcattgactaaatgaaaacatcgtcgattttacagtattgtaatattgactgtcttgttcttaaatgatatc-ttgtgtctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG
                                                                                       | ||||       | | |   ||| ||  ||   ||  ||    | |||| | ||  |||  ||||    |   |||||||||||||||||  | || |||||||| |||||||||||||||||| | |||||| |||| ||||||    | || || ||||| |||||||| || |
--------------------------------------------------------------------------------------gtaaaaa-------gctctcgaagttttcgaaacctggttg----gatcttcactgtgatcgctgtgatgttttccagAGTGACAACATGACTGATAAATGGCACGTTTACATGACAAAGGATGGACGAATTTCCTTGGCTGGATTGAATCTAGCCAAGTGTGACTACCTTGCGGACG

upper sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ05582 (Selaginella moellendorffii), 3'ss of exon 8
gtaattgactactgttattacaacttcttgcatgtgatcaacttgtggcttttatacactatgttgagtcctatttcattgactaaatgaaaacatcgtcgattttacagtattgtaatattgactgtcttgttcttaaatgatatc-ttgtgtctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG
                                                                                       | ||||       | | |   ||| ||  ||   ||  ||    | |||| | ||  |||  ||||    |  ||||||||||||||||||  | || |||||||| |||||||||||||||||| | |||||| |||| ||||||    | || || ||||| |||||||| || |
--------------------------------------------------------------------------------------gtaaaaa-------gctctcgaagttttcgaaacctggttg----gatcttcactgtgatcgctgtgatgtttttcagAGTGACAACATGACTGATAAATGGCACGTTTACATGACAAAGGATGGACGAATTTCCTTGGCTGGATTGAATCTAGCCAAGTGTGACTACCTTGCGGACG

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|16346926|gb|BI972521.1|BI972521
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACGGGCTTGAACACGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACGGGCTTGAACACGAACCAGgtaattgact ... ctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
EST: gi|51345152|gb|CO985885.1|CO985885
EST:     TACTTAAGCAGATAGGCATGTTCTCATTCACGGGCTTGAACACGAACCAG                         AGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG
genomic: TACTTAAGCAGATAGGCATGTTCTCATTCACGGGCTTGAACACGAACCAGgtaattgact ... ctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtattgtaatattgactgtcttgttcttaaatgatatcttgtgtctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG
          tattgac  putative branch site (score: 2)
                                            tctctcatc  putative PPT
                        ttcttaaatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgactactgttattacaacttcttgcatgtgatcaacttgtggcttttatacactatgttgagtcctatttcattgactaaatgaaaacatcgtcgattttacagtattgtaatattgactgtcttgttcttaaatgatatcttgtgtctctcatcagAGTGACAACATGACAAACAAGTGGCACGTATACATGACAAAGGATGGAAGGATTTCCCTGGCAGGATTGTCATTGGCTAAATGTGAATACCTTGCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG