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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatcattgatagtaccctatgaacatctttgaccttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG

Basic information

species Glycine max
transcript GLYMA01G03610.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 4
ttcatcattgatagtaccctatgaacat-ctttgaccttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG
|||||||| || || | || | ||| |||| | || || | | | | || || | || | || | | |||| |||||||||| || |||||||||||||||||| ||| |||| || |||| |||||||| ||||| || || ||||||||| |||||
ttcatcatgttcgatattttagataaatgcattgcggttatggcctacatatgatgctgagcccaatg-gtgccatcatgtgtcccattttctgtttgtagGTGGTTCTAGGAGGTGGTCAGGATGCAATGAATGTGACTATGACAGATCGCCGTGCTGGTAAATTCGAGGCTAAATTCTATCACAAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G46280.1 (Arabidopsis thaliana), 3'ss of exon 5
ttcatcattgatagtaccctatgaacatctttgaccttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG
| || | | ||||| || | | || | | | | | | ||| || | || | || | ||||| ||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||| || |||||||| || || || ||||||
---gtatgcactaatgcttcatgaa---attcaatttcgaatcccagaatcagcaaggcatgatgt-tatctttgtgaatgtttctgctctctcttttagGTTGTACTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 6
ttcatcattgatagtaccctatgaacatctttgac-cttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG
| || | || | | | || || | | | | | | | || | || |||| |||||| || | || | ||||| || |||||||||||||| |||||||||||||| ||||| ||||||||||||||||| || |||||||| || || || |||| |
gtatgcactaatgcttcttgaaattcaaattcggttcccaaaagcaacaagtcttgatgttatctttgtgaatgtttctgctctc---gctcttt---tagGTTGTGCTTGGAGGTGGTCAAGATGCATCAGCTGTGACTACCACTGATCATCGTGCTGGGAAGTTTGAAGCTAAGTTTTACGACACG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 5
ttcatcattgatagtaccctatgaacatctttgaccttatattttttatttggtcatatgttccttgt--atgattttctgaattccgtgtcctgtgtgt-----agGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG
|| || || | | | ||| | || | | | | || | | |||| ||| | || || | | || | ||||| |||| ||||| ||||||||||| ||||||||| ||| || || ||||||||||||||||| || ||||| || ||||||||||| |||
--tatacttacatgtgttgggtatataaattta----cagatggtggaaatagatat-cgctgattgttcatgctgtttctaactttgattcttttgtgttctccagGTAGTACTAGGAGGTGGTCAAGATGCATCACATGTCACAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG

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|209726207|gb|BW659572.1|BW659572
EST:     CACAGAACGGCCGGGTCA-TGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: CACAGAACGGCCGG-TCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|193383818|gb|FK353015.1|FK353015
EST:     TTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGCGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: TTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|208047672|gb|GD849697.1|GD849697
EST:     TCAATGCAGTTGCAATGTCACCTCTACTTGATTCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCA
genomic: TCAATGCAGTTGCAATGTCACCTCTACTTGA-TCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCA
EST: gi|213604401|gb|DB983489.1|DB983489
EST:     CACAGAACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: CACAGAACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|207842792|gb|GD816436.1|GD816436
EST:     TCACAGAACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: TCACAGAACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|209726208|gb|BW659573.1|BW659573
EST:     TCACAGAACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: TCACAGAACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|193639608|gb|FK587053.1|FK587053
EST:     TCAATGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: TCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|193449022|gb|FK413817.1|FK413817
EST:     CGGCCGGTCAATGCAGTTAGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: CGGCCGGTCAATGCAGTT-GCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|193552832|gb|FK510723.1|FK510723
EST:     CGGCCGGTCAATGTCAGTTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: CGGCCGGTCAATG-CAG-TTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|208273808|gb|GE069302.1|GE069302
EST:     CGGCCGGTCAATGCAGTTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: CGGCCGGTCAATGCAG-TTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|193481882|gb|FK445209.1|FK445209
EST:     TCAATGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTCGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: TCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
EST: gi|207774007|gb|GD745523.1|GD745523
EST:     ACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCAT                         GTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT
genomic: ACGGCCGGTCAATGCAGTTGCAATGTCACCTCTACTTGATCATgtatgtatct ... ctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG
                      tatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatcattgatagtaccctatgaacatctttgaccttatattttttatttggtcatatgttccttgtatgattttctgaattccgtgtcctgtgtgtagGTGGTACTTGGAGGTGGTCAGGATGCATCAGCTGTTACTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC