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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttttattgccattgaccatgccattttttccttttgaatatgtcttttgatgactgaatcttgtgtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA

Basic information

species Glycine max
transcript GLYMA20G11330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
gta-attgttttattgccattga-----ccatgccattttttccttttgaatatgtcttttgatgactgaatcttgtgtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
||| ||      ||   || ||      ||| | |    |||   ||  | ||  | | || ||| ||   | || ||||   |||| | ||||| || ||||||||||| || | ||| ||  ||| ||| || ||| | ||||||||||| ||||||||||| || |||||||||||||  || |
gtatatacacacatgaacactggaagccccaagtcggccttttacttctattagttttattaatgtcttttttttctgtt---acagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 6
-------gtaattgttttattgccattga---------ccatgccattttttccttttgaatatgtcttttg---atgactgaatcttgtgtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
        || ||||||| ||    |  |         |  ||   | |    | | |   |||  |  | |   |||  |   | ||| | ||||||||||||| || | ||| ||||| ||||||||| |||||||||| ||||| ||||| ||||| || ||||||||||| ||||| |||||||||| |||||| |
gtaagttctatttgtttttttttattcaaggataaattctgtgaagtctacctcatctacttatcaccatcgtctatgtttctcttttg-gattaaacagTTACCCCAAATAAACCCTGGTTTCAACAACGCTCCATTTAAATTCACGAAGTATTCAAACGCGTATATGCTTGTTTATATTCGTGAAAGTGCCAAGGAGA

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 2
gtaat-tgttttattgccattgaccatgccattttttccttttgaatatgtctt---ttgatgactgaatcttgtgttta---aacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
||||  |  |||||  | | ||  ||| | ||    | |||  | |  ||| ||   ||      |   |||| | | ||   ||||||| || || | ||| ||||| ||||| ||||| |||||||| ||||| ||||| || ||||| || |||||||| ||||||||||| |||||||| || |
gtaacattctttatgacaaatgttcattcaatacaatacttgcggacttgtattaactttcctcttatttcttctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACGCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGA

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 12
---------------gtaattgttttattgccattgaccatgccattttttccttttgaatatgtcttttgatgactgaatcttgtgttt------aaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
                 ||||  || | | | ||  |   | |           | | ||| |  |  ||  ||  | | |||| |  ||       ||||||| || || | ||| ||||| ||||| ||||| ||||| || ||||| ||||| |||||||| || |||||||| ||||||||||| | ||||||||| |
gtaaaattctttataacaattcattcaatacaatacagt-tacttgaggacttgtataaattttccacttattgcttaactcttattctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACACCATTCAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTATATACGTGAGAATGACAAGGATA

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
------------------------gtaattgttttattgccattgaccatgc--cattt---tttccttttgaatatgt-cttttgatgactgaatcttgtgttta--aacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
                         |||||  |||    | |||    || |  || ||   | | |||| |||    | |||||    |||    ||  |  | |  ||||| | || ||||||||||||||||| || ||||| || ||||| || || ||||| |||||||| || ||||| ||||||||||||||||||||||||||||
gtaatgttttcttgagtttagctcataatt--tttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

upper sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 10
gtaattgttttattgccattgaccatgccattttttccttttgaatatgtcttttgatgactgaatcttgtgtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
                              | | || |||   ||| | |  |  |||   ||  |  |||| |    ||| | |||||| | |||||||| |||||||||||| | || || || || ||||||||||| |||||||||||||| ||  | || ||  | || || ||  
-----------------------------gtatgtttcttgctaat-ttttgtgcgatttttgc-taatgtgct-gcgcagCTTCCACAGGCGAATCCTGGTTTCAACAACACTGCGTTCAAATTTACGAAGTACTCAAACGCTTATATGCTTGTTTACGTCCGAGAGTGCGATAAAGATC

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|151412634|gb|EV282446.1|EV282446
EST:     AAGAAGATAATAAAAGAGCATTAGAGGAGCAGTATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCCGGATTCAATAACACCCCATTTAAGTTCACCAAA
genomic: AAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAGgtaattgttt ... gtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAG
EST: gi|254341879|gb|GR853016.1|GR853016
EST:     AAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAG
genomic: AAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAGgtaattgttt ... gtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAG
EST: gi|254341880|gb|GR853017.1|GR853017
EST:     AAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAG                         TTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAG
genomic: AAGAAGATAATAAAAGAGCATTGGAGGAGCAATATGGTGGTGAGGAAGAGgtaattgttt ... gtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccattttttccttttgaatatgtcttttgatgactgaatcttgtgtttaaacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA
                         ttttgat  putative branch site (score: 4)
            ttttgaatat  TA-rich tract