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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

Basic information

species Glycine max
transcript GLYMA01G03610.1
intron # 6
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 6
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
gtaagtttttttttttt--ttcctttactatgtttagttctc--taatgata-tgtaacatctactt---attttgctttttatttca---------tatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
|| |||| |||     |  || || |  |||||||   |      ||||||| ||||   |    ||   || ||  |||||  || |          | || |  || | ||  | ||||| | ||||| |||||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| |||||||||   ||
gtcagttctttgcacatggtttctatcttatgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactt--tcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
gtaagtttttttttttt--ttcctttactatgtttagttctc--taatgat-atgtaac-atctactta---ttttgctttttatttcatatttg------ttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
|| |||| ||      |  || |  |  |||||||   |      ||||||  |||    ||||  | |   || |  |||    ||||    ||       |||   |||  ||||||| | ||||| |||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||||| ||||||||    ||
gtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 5
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctt------tttatttcatatttgtta---ttcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
|| | ||||   ||       | ||      ||| |  | |  || ||  |       ||||    |||||      |||    |||  || |||    |   |   ||||||| | ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||||||    ||
gtgatttttcagttcacagaatataaatgccttactctttttgtgttacatcttgctaactttgcatgcttacaatatttgaaccattattattaaaacttgctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 5
-------------------gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
                    ||| || |       || |   |  | |||| | |||  |  | |  ||  | |  |||   |||||   | |  |   ||    ||  ||  ||  ||||||| | ||||| |||||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||    ||
gtaatttctttttcagttaataaattatcaaggcattactccttttgtgtt-acttccttgctaacttggtatacttacaatttttgaactgttctgattaaaacttgctctctt--ttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
           ||  | || |  ||  |   ||  || | |||  |  |||||| |  |   |       | | | |   |||||| | ||    |   |||||||| ||||| |||||||| || || ||||| ||||||||||| |||||||| ||||| || |  |||||||| || ||
----------gttagtgttgcagtaaaacagtt--ttatttaaaaacttgtaacctgga---aagagatatgtaactgtgtatttggtcttataatatatagATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgat---tagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
     |  | ||| |  |     |  | |  || |     |  | |  || || ||  || |||||   |     | | ||  ||||  ||  | | ||   |||||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||||| ||||| || || |||||||| || ||
---gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaaatacacatatttaaataaccgtgt-atcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

upper sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
    ||  |   | | | |   |  || ||| |   | | |     | |||   | ||  || ||  | |  |||  | |||||  |    ||||||||||||||||||||||||||||||| ||||| |||||||| |||||||| || ||||| || || || |||||||||||||| ||
----gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactg-ttgttgggttaattaaattatattcctg---catttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG

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|193383818|gb|FK353015.1|FK353015
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|208047672|gb|GD849697.1|GD849697
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTNTAAAAAGGGCATTTTGGACCAATTAA
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAA-GGGCATTTTGGACCAATTAA
EST: gi|213604401|gb|DB983489.1|DB983489
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATAATATGACAAG                         ATAAATCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|209726208|gb|BW659573.1|BW659573
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|193449022|gb|FK413817.1|FK413817
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|193552832|gb|FK510723.1|FK510723
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|208073965|gb|GD871550.1|GD871550
EST:     TCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: TCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|15662606|gb|BI699977.1|BI699977
EST:     ATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: ATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|208273808|gb|GE069302.1|GE069302
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAAATTGGGGGT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAA-TTGGGGGT
EST: gi|193481882|gb|FK445209.1|FK445209
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|193312788|gb|FK280856.1|FK280856
EST:     TCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: TCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
EST: gi|207774007|gb|GD745523.1|GD745523
EST:     CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAG                         ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT
genomic: CTACTACTGATCATCGTGCTGGCAAATTTGAAGCCAAATTCTATGACAAGgtaagttttt ... atttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG
 atgtaac  putative branch site (score: 3)
                                          ttcattt  putative PPT
             ttattttgctttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA