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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA

Basic information

species Glycine max
transcript GLYMA09G22600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
tgccttcatcagtcatattgcaactatttcaattaa--acagctttgaaggatttaatagaacttagatttgaaa-tttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
    ||| |   |   ||| |||   |    | ||    ||      |   || || ||   | |  |||  |   |||||| | || | |   || |||||||||| || || || ||| |  |  ||||||||||| ||||||||||||| ||||| ||||| || || ||||||||||||||||| ||||| ||||||||
---attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgagtacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090172_T02 (Zea mays), 3'ss of exon 1
-tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaat--tggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
 |   ||||  ||  | | || |  |   |    | || | || | | | || |  |   |     ||||  |   |||  |  |  ||  ||    |||||||||| || || || ||  |  |  |||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||
ttttgttcacaaga-acaatggatttgaatt--ctgaatacctgttatgcatgttgtgtgataataatttagatcataccttgttctatggtgtcttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATA

upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 1
-tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaat--tggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
 |   ||||  || || | || |  |        | || | ||   |   || |      |     ||||  |   |||| |  |  ||   | |  |||||||||| || || || ||  |  |  |||| || ||  | ||||||||||| ||||| ||||||||||| |||||||| ||||| || ||||| ||||||| 
ttttgttcacaag-cacaatgaatttgaact--ctgaatatctgctattcatgttgcttgataataatttagatcatactttgttctatggcgttttctgcagTTCCCAGAAACTTTAGGCTGCTAGAAGAACTAGAACGTGGTGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATT

upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G70660.2 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------------------------tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccc--------tgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
                                                                      |  |||| | ||   ||  | ||| ||||  |||| |||| ||   | |      || | | | |  ||||   ||  | |  || |||| |           ||||||||| || || || ||||||||| ||||||| || ||||||||||| |||||||| ||||| || || || |||||||||||||| ||||| || || | 
gtaagtctaatccaatttttttttttgattcgattagtctctttgatttggaatctagggttttactttattgcttccttaggtttaaagtaacgattttgattacacagattgcgaagtcactctatatcgttg--ttgatcatttgtatctttgattgattttgtgtggtttgcagTTCCCAGAAACTTTAGATTATTGGAAGAGCTAGAAAGAGGTGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTT

upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
tgccttcatcagtcatattgcaactatttcaattaaa-cagctttgaaggatttaatagaacttagatttgaaatttactctt-cttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
     | ||| |    || |   | |||     || | | | | || |  ||   ||   | || |    || |||||      ||| |||      || |||||| ||||| || ||||| ||| |||||||||| ||||||||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || ||
gaatgtgatcggatccatggtctcgattaggtatatatctgatctgtaaaat--gatttgatttgggggcgatatttataagagcttgattttgtgatgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 1
tgccttcatcagtcatattgcaactatttcaattaaacagc--tttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
     || |     || ||     | ||     || |  |   |||||  | ||  ||  |    ||     | || |       ||  | |     ||||||||| ||||||||||||||| || |||||||||||||||| || ||||||||||| ||||||||||| || |||||||||||||| ||||| || |||||
--ttatcttggaaaattttctggttgttgttgctacatggtcttttgagtgcttgcatgcatagcaggagatatatctttgtgattttgtggtcatatgcagTTCCAAGGAATTTCAGATTACTGGAAGAGCTTGAGAGAGGGGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATA

upper sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
tgccttcatcagtcatattgcaactatttcaattaaacag----ctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
|   ||||   |    |    || | ||    ||| |       ||| | |   | |  |    |||   ||| |||| |     | |  |       ||  |||||||||||| ||  |  |  |  | ||||||||||| |||||||| || || || ||||| || || |||||||| ||||||||||  |||||  ||| 
ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaa----ctatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT

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|298168826|gb|HO009756.1|HO009756
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCGGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|6071962|gb|AW101349.1|AW101349
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|33387487|gb|CA850694.1|CA850694
EST:     TAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: TAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|298193121|gb|HO033555.1|HO033555
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|21285722|gb|BQ473593.1|BQ473593
EST:     TTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: TTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|193401185|gb|FK365466.1|FK365466
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|9898614|gb|BE607582.1|BE607582
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|22522487|gb|BU081298.1|BU081298
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
EST: gi|19269626|gb|BM885882.1|BM885882
EST:     CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCG                         TTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA
genomic: CTTCGAATTTTTCATAATCGTAATGGGTTCCGAAGGATCCAGCGTTGTCGgtgagcattc ... gtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggatttaatagaacttagatttgaaatttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA
                                    tcttaat  putative branch site (score: 3)
                                              tccctgc  putative PPT
     tttaatagaacttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccttcatcagtcatattgcaactatttcaattaaacagctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
tgccttc
- - - - - - - - - tgcaact