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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGGGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattatgcaataaaataacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttgttcaatcatacactcccccgtctac...

Basic information

species Glycine max
transcript GLYMA08G13320.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13320.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g65450.1 (Oryza sativa), 5'ss of exon 5
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTT----CTTCTCGTG-----GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgt-aata-ttatgcaataaaat-aacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttgttcaatcatacactcccccgtctac
|| ||| |||| ||||| || || || || | | || ||||||||||||||||||||| | || |||||| ||||||| ||||| | || | | || | || | | | ||| || || ||| ||| | | || | | ||| || || || ||
---------GGATCACTTGGCGATGATAACTGTGCAATCTGAAAACCTGTCAGAAAAGAAAACTTTTGATTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCCGAGgttagtagtggcgtggtactgtgaatttgtgactgattctc---attgaa--ttatttgctcattgct--tctgtttctttcat-atgcag------------

upper sequence: GLYMA08G13320.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G114172_T03 (Zea mays), 5'ss of exon 4
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGG---------GGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgt-aatattatgcaataaaataacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttg---ttcaatcatacactcccccgtctac--
|| ||| |||| ||||| || || || || || | | ||||| ||||||||||||||| | || |||||| ||||||||||||| | || | | | | |||| | |||| | ||| | | | ||| | || | || | || | | |
---------GGATCACTTGGCTATGATAACTGTGCAATCTGAAAATCAAAGTAGAAAGAAGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactctatttctgtgct-cgtattaccaatttaat--gtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgt-cttctccatatgcag

upper sequence: GLYMA08G13320.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G427526_T01 (Zea mays), 5'ss of exon 1
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGG---------GGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattatgcaataaaataacacgccatttattttcttaatggaaagttaa-tagaattatgttagcatatttgttcaatcatacactcccccgtctac------------------------------------------------------------------------------------
|| ||| |||| ||||| || || ||| || ||| | | | ||| | ||||||||||||||| | || |||||| ||||||||||||| || ||| | || | | || || | || ||| || || || | ||| || ||| | ||| | | | || |||| |
---------GGATCACTTGGCTATGATAACTGTGCAGCCTGAAAATCGAAGTAGAAACAAGATTTTTCACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgt--tagtattctatttatttctgtgc---ttgtgttaccaatttaatgtgaaactgggttaggtcctcat-ctaattctttgccgcttgctcctgtcttccccatatgcagtagcctgtactacaacgaaaagaacaccatcatgtttgatgatctaagaaggaatttcgtcatgaatccacag

upper sequence: GLYMA08G13320.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv12s0035g00640.t01 (Vitis vinifera), 5'ss of exon 5
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGGGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattatgcaataaaataacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttgttcaatcatacactcccccgtctac---
|| ||||| ||||| | |||||||| || ||||| | |||||||||| ||||||||||||||| ||||||||||| |||| | | || |||||||| || | || | | | | || ||| | | | || | | |||| || | || | | |
AGCTCTTCTGGACCATTTAGCAATGATTACAGTTCATTCAGATTCTCGTGGGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatattccatttttttttttcctcccctagtttttcttttctct-tcgtcttcatcaaatc--catagctggttaaataagtctttattaaagaaaagg

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|16347120|gb|BI972715.1|BI972715
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACGATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|207847520|gb|GD820113.1|GD820113
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|193685533|gb|FK627037.1|FK627037
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|208178046|gb|GD976473.1|GD976473
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
EST: gi|208095905|gb|GD894175.1|GD894175
EST:     GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAG                         TTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT
genomic: GGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattat ... tctatttcagTTCTACAATGCTTCAAATACTATCATGTTTGATGACCTTAGAAGAAATTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGGGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattatgcaataaaataacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttgttcaatcatacactcccccgtctac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc