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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT

Basic information

species Glycine max
transcript GLYMA18G05730.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 2
ctcctaaagtttcctgggggtttcaaattcatt----gattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatat-ttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
| | | |||| ||| ||| | ||| || |||| | |||| | || | ||| | | | ||| | ||| || | || |||| || | ||||| || |||||||| ||| | ||||||||||||||||| || || ||||| || |||||||||||||| ||||| |||||| | |||
-gctttatgttt--tggatgttgagacttcgtttgtagattttctatggtttt-tgggcatactagttcttttcttgatgaagttcttt--tattcatttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCAGCTATCATATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 2
ctcctaaagtttcctgggggtttcaaattcat-tgattgtatat-gttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
| | ||| | | | | | | | | | | |||| | | || | | |||||| | || | | | | || |||| || ||||||| |||||||| || ||| | ||||| |||||||| || ||||| || || ||||||||||||||||| |||||||||||| | |||
ttagtggttattcgtagatatatgttgtcgacataaaaatttgcagttccttttttcggct--gttcaacattagtcagtcatattcttaactcct-ttgtagGGCCCTAGAATGGTGCGTGATGTGTTCCGTTTGGCTAAGGAGAATGCTCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGCTTTG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatctt----ccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
||| || | ||| ||| || || | | | ||||| | || | | |||| | | || | | | | || | || |||| || ||||||| ||||| || || ||| | || || ||||||||||| ||||| || || ||||||||||||||||| |||||||||||| | |||
--cctgtcgtggacataaaattttgcatttttttcttcttttcagctgt-tcaatatatcagtcctat-tcttgacgtgttatgatctttctacttct-ttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 2
ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
| | || | |||| | | || | || | | ||| | | | | | || || | | || | | ||||||| |||||||||||||||| || |||||||| || |||||||| ||||||||||| || ||||||||||||||||| || || || ||||| |||
tggttttaattgttttatcttttctagattgccaatattgc-tgcaatacccttaaattttaatttatctatatatatattttttttctcttgttatcaagGGTCCGAGAATGGTCCGTGATGTTTTCCGTCTTGCCAAGGAGAATGCTCCTGCAATTATCTTCATTGATGAGGTTGATGCTATTGCTACCGCTAGGTTTG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 2
ctcctaaagtttcctgggggtttcaa-attcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccc--tgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
|| || | || | | | |||| | | | | | | | |||| || | || || || |||| | || | || | | ||||||| || ||||| ||||| ||||| || || || || ||||||||||| || ||||| || ||||||||| |||||||||| || || ||| | |||
----caattctttcaggagatcttgttgttcagcgttcatgtttctgaatgccaattgtgctgtgcttgatattaaaataaacgaaatgtaaattttgtcatagGGTCCCCGCATGGTACGTGACGTATTCCGACTGGCAAAGGAGAATGCCCCAGCCATTATCTTCATTGATGAGATTGATGCAATTGCGACAGCTCGTTTTG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 2
---ctcctaaa-gtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
| |||| |||| |||| | || | |||| | |||| | | || | | | | | | |||| | || || | | ||||||||| || ||||| |||||||| || || || || || ||||| ||||| || ||||| ||||||||||| |||||||||| || || ||| | ||
actttattaaatgttttctggaattatcgtagtcatagcttgtttttatt--agacgccagct--aacccgtgttagaaaatatgtaatgtaatgtg-gtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 2
-ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
| | | || || | || || || |||||| | | | || || | | | | |||| | || || | |||| |||||||| || ||||| ||||||||||||| || || || || |||||||| || ||||||||||||||||| |||||||||| || || || | ||
gtattttatgcactctcaggaaacgtagttttgaaatggtctatgttataggacgtcggtt-gaactatgtttgagtatctcgcatgtaatgt-tattacagGGTCCCCGTATGGTGCGTGATGTATTTCAACTGGCAAAGGAAAATGCCCCAGCTATTATATTTATTGATGAAATTGATGCAATCGCAACAGCCCGTTTCG

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 2
----ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-
| || | | ||||| | || || | | | | | ||| ||| || ||| || || | | | | |||| |||||||| || ||||| ||||||||||| ||||| || || ||||||||||| || |||||||||||||||||| |||||||||| || || ||| | |||
ttatgttgcaagataatcctttcgtttctggta-atcaatcattttaaaccctcgggcttattttcagcttca-cttgaactcatgtgtagcct---tattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCAGCCATTATATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTG

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|208132889|gb|GD931270.1|GD931270
EST:     GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGA                         GGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
genomic: GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcattt ... ttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
EST: gi|5607016|gb|AI901114.1|AI901114
EST:     GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGC-G-                         ---TCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
genomic: GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcattt ... ttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
EST: gi|58022279|gb|CX709020.1|CX709020
EST:     GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGA                         GGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
genomic: GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcattt ... ttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
EST: gi|5508931|gb|AI855489.1|AI855489
EST:     GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGG-G-                         ---TCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
genomic: GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcattt ... ttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
EST: gi|16342518|gb|BI968113.1|BI968113
EST:     CTTTCATCAGGG-TGNNGGGATCTGAGTTTGTGCAGAAGTATC-T--T--                         GGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
genomic: CTTTCATCAGGGTTG-TGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcattt ... ttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
EST: gi|17401263|gb|BM178045.1|BM178045
EST:     GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGA                         GGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC
genomic: GCTTTCATCAGGGTTGTGGGATCTGAGTTTGTGCAGAAGTATCTTGGTGAggtatcattt ... ttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT
                                tcttccctgccattt  CT-rich tract
 atttatatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT

- - - - - - - -gggggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcttc