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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataagcagtacactatagctttttttttttttttattgaattctcttagttttcttcatctcaacaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

Basic information

species Glycine max
transcript GLYMA05G05860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
ataagcagtac-actatagctttttttttttttttattgaattctcttagttttcttcatctca---acaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA
       |||  |    | |||||  |   |||  | | | || |  || |  |    |         ||   ||   |  | ||| | |||  |||    ||||||||||||||| |||||| |||| || ||| | ||||||||||| || || ||||| || ||||||||||| || | |||||||||||
-------gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA

upper sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 2
ataagcagtacactatagctttttttttttttttattgaattctcttagttttcttcatctcaacacc-ttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA
             ||| |    |  |  |   ||  |    | | ||     |    ||||    ||  || || ||     | ||||   ||  |  ||||||||| ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || |||||||||||||| |  ||||||||||
------------gtatggtgactactactgcattcatagcctgt-ttgccccttgagatctatggactgttgaccttatgcatgttttattttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
ataagcagtaca-ctatagctttttttttttttttattgaattctcttagttttcttcatctcaacaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA
       ||| |  ||   ||  |   |   ||    || ||   |  | | |  |  |   |    | || || ||     | | ||   ||  |  ||||||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || |||||||||||||| |  ||||||||||
-------gtataattactactactgcatccgttagcctgtatggccccattgtgatcta---cggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
ataagcagtacactatagctttttttttttttt--tattgaattctcttagttttcttcatctcaacacc-ttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA
    | |  |   |    || |||   ||||    || ||||   |   | |     |||| |    |   || || |  |         ||||   |||||||||||||||||| || ||  |||| || ||||| ||||| ||||| || ||||| || || |||||||| ||||| |||||||||||||
----gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcat--atgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA

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|7146015|gb|AW507937.1|AW507937
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|21995147|gb|BQ786675.1|BQ786675
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|8284612|gb|BE022171.1|BE022171
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAGAGATTTAGAAGTCTTATTCCAAGCTACATTAA
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|192325163|gb|FK017534.1|FK017534
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|298193040|gb|HO033474.1|HO033474
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|13252783|gb|BG363686.1|BG363686
EST:     TTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: TTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|192321239|gb|FK014329.1|FK014329
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|193335501|gb|FK300201.1|FK300201
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGG
EST: gi|192322379|gb|FK014620.1|FK014620
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
EST: gi|192321240|gb|FK014330.1|FK014330
EST:     CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG                         GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG
genomic: CTGTCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatgtt ... tttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttttcttcatctcaacaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA
                            ttttaat  putative branch site (score: 3)
                     ccttcacttttaattt  CT-rich tract
                       ttcacttttaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataagcagtacactatagctttttttttttttttattgaattctcttagttttcttcatctcaacaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

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