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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG

Basic information

species Glycine max
transcript GLYMA13G40960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
---tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
|| |||| | ||| | | | | | || || | || | | ||| ||| | ||||| || | | | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
gtatgctagatctctgtta--catgagaggtggtatattttcatagttt-----ttcctga-----tattggt---gtttgtgattgtctg------taacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
-tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
| | || | ||||| | | | | | || || | || | | ||| ||| | ||||| || | | | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
gtatgctagatctctgctgcatgagaggtggtatattttcatagttt-----ttcctga-----tattggt---gtttgtgattgtctg------taacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattacttta-cagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
|| ||| | || ||| || ||| || ||| | | | ||| || || | ||| | | |||| | | || || || ||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
-gtatactagttctc-tgc-tctgtgagagacagtacgtt--gtttaatagtttttcctgg--tatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 5
-tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
| | || | ||||| | | | | | || || | || | | ||| ||| | ||||| | | | | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
gtatgctagatctctgctgcatgagaggtggtatattttcatagttt-----ttcctga-----tattggt---gtttgtggttgtctg------taacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 6
-tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
| | || | ||||| | | | | | || || | || | | ||| ||| | ||||| || | || | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
gtatgctagatctctgctgcatgagaggtggtatattttcatagttt-----ttcctga-----tattggt---gtttgtgattg------tatgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 2
-tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
| | | || | ||||| | | | | | || || | || | ||||| ||| | ||||| || | | | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| |||| ||
gtatgctacatctctgctgcatgagaggtggtatattttcatagttt-----ttcttga-----tattggt---gtttgtgattgtctg------taacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTAGAGCTAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
| ||| | | ||| | |||| | | | || || || | || | || | | | |||||||| ||||| ||||||||||| ||||| |||||||| || ||||| ||||| || ||||||||
-----------------gttcgtgtgaatatagatatattct-catatcaccttcatataatcagaatcgttagttactgatctaata-tgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
tgtctacctcctgtcatgcatcattgatcgaaagtt-ctctctgcttatc--tgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG-----------------------------------
||| | | || || ||| ||| | | |||| | | || | |||| ||| || | | | | | ||||| ||||| |||||||||||||||||||| |||||| | || || || |||||||| ||||||||
--------gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
----tgtctacctcctgt-catgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
||||| | | | | || | | ||| | | ||| | | |||| | | | | | || ||| || | | | || |||||||||||| ||||| || ||||| |||||||| ||||| || ||||| || ||||| ||||||||
ttgacgtctagattttttgtgttcaatgtcagt--gcagtcatttgaacttgtgaattattgaga-attgtctgact--tttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG

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|151406393|gb|EV276208.1|EV276208
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttt ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG
EST: gi|151404362|gb|EV274172.1|EV274172
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttt ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG
EST: gi|213590294|gb|DB963857.1|DB963857
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttt ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG
EST: gi|19052776|gb|BM731443.1|BM731443
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttt ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG
                       atctaat  putative branch site (score: 3)
 ttacttt  putative PPT
 actatatatctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -ctacctc
- - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - ctctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagac