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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgccaatgcttctcattatcttctctaatcatcaaattaaatatttcttctagattggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

Basic information

species Glycine max
transcript GLYMA17G01360.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
gtttgtgc-caatgcttctcattatcttctctaatcatcaaatta-aatatttcttctagattggttttaatgattgactgtggttgaaaatgtttcgtaatactggggcca--tcaact--caatttttggatc-tgctatgatatttttat-------cagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
|| ||  | | ||  ||| |  |  ||| |   ||   || |||  ||  |     |  | || ||   | |||| |  ||  |         || || |  |  |  | ||  | ||||   |||  |  |||| |||| | || ||| |||       |||||||| ||  |   ||||||||| ||||||||||| ||||||||||||||| | || || |||||||| || |||||||| || |
gtatgcacactatagttccctgtcacttgttggatacccagattggaacctaagaacgggctttgtggaagtgat-gtttgcagcatgtttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttttactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 5
gtttgtgccaatgcttctcattatcttctctaatcatcaaattaaatatttcttctagattggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                               |   |    ||||      |||   ||||   || || ||  ||| ||||| |||   | |       |||| |    ||    ||           |||   |  |  |||  | ||||||| ||  |    ||||| |||||||||||||||||||||||||| ||| | || ||| ||||||| || |||||||| || |
-------------------------------acctacagtattaggagcatctgggagatgtcttatattg--tgattgtggctgatcgtat------gtacttgcatgatttggtcg----------ctgtcttttttctttgcttagGTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 12
gtttgtgccaatgcttctcattatcttctctaatcatcaaattaaatatttcttctagattggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                                   |     |||   ||  ||   ||||   || |||||  ||  ||||  |||     | |  |  |||| |   |||  | | |||   ||  |||  | |  |  ||   ||||||||| ||  |    ||||| || ||||||||||||||||||||||| ||| | || ||| ||||||| || |||||||| || |
-----------------------------------acagtgttaggaatacctgggagatatcttataatg--tgtttgtgactga-----tcttatg-tacttg---cat-gatttaatcgctg--tcttttttttttcttggctcagGTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgtgccaatgcttctcattatcttctctaatcatcaaattaaatatttcttctaga--ttggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                                    |  | |  |  |||||  ||| |   || |||  ||   |||   |  |    |   ||| |||| ||| |    ||   || |   |   |||  | ||   ||||     |||||||| || |||  ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| |
---------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataat----agcctttggtaa-actag---tatgtgcttagaatg-agatgagttaacttattggcg-cagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
--------------------gtttgtgccaatgcttctcatt--atcttctctaatcatcaaatta--aatatttcttctagatt---ggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgcta-tgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                      |  |     | ||| |   |   |||||  |  |  |||  ||   ||||| || |   | ||   |  || ||    |   | |  |    || |||   || || |       | |||  | |||||| |  || |  | ||  | |  ||||||||| ||| ||| |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| ||||||||||||||||
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggtt--atagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG

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|193610338|gb|FK566168.1|FK566168
EST:     CTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTGGAAGAATGGACTGTTGGTGGAACTGCA
genomic: CTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|19348946|gb|BM893478.1|BM893478
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|58019435|gb|CX706177.1|CX706177
EST:     ATGGTGCTGCAGCCNTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|7924124|gb|AW830150.1|AW830150
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|254317928|gb|GR832096.1|GR832096
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|57574880|gb|CX547855.1|CX547855
EST:     ATGGTGCTGCAGCCNTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|5342423|gb|AI794707.1|AI794707
EST:     ATGGTGCTGCAGCCCTTCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|193426110|gb|FK390397.1|FK390397
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcca ... tttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                                             tttttatc  CT-rich tract
                                      tatgatatttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgccaatgcttctcattatcttctctaatcatcaaattaaatatttcttctagattggttttaatgattgactgtggttgaaaatgtttcgtaatactggggccatcaactcaatttttggatctgctatgatatttttatcagGTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA