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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctgtgatgcatcttgattcattcagctatgagatatataattgtccacttttaatacaatttactgtgtgatattgaccttaacctttcacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG

Basic information

species Glycine max
transcript GLYMA09G00430.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 15
------------------------------------------------------atctgtgatgcatcttgattcattcagctatga--gatatataattgtccact-tttaatacaatttactgtgtgatattgaccttaacctttcacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG
                                                      |    | |   ||  | ||    |||  |      ||| |  || |||||  | |||| |  |   |   |||| || |     ||    |||||  || ||||||||||||||||| ||||||||||| | ||||||||| |||||||||    | |||
gttaatatatctcgtacactgatgtactggtgttccccatatttgatttttctgaataataacttatgataatcttgtcatttgctgccgattttcaaatgtcctttatttagttaagaatttggtgtcatttactgttttttttttcatgtc-cagCTTGGGTACACCAAGAAACAAGAGGAGAGACATTTTCGAGGTGTTATTGTCCTGGAG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 15
------------------------------------------atctgtgatgcatcttgattcattcagctatgagatatataattgtccacttttaatacaatttactgtgtgatattgaccttaacctttcacttca----cagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG
                                           | ||  ||| || |  |  |  | || | |   | || || ||      | ||  |  |  |    ||||| | ||   | | | || |   |||     |||||||||||||| || ||||||||||| | ||||||||| ||||| || ||  | |||
gttaatcagttcttcagaacatttcttttgaactcttgatttgtttgatatgtatgtgaaagcccttaggttttcaa-atgtatttcatggttcttgtttgatatgtgggtgtggttttattcattatctgttgtttctatgccagCTTGGGTACACAAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 15
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
-----------------------------------------------atctgtgatgcatcttg--attcattcagctatgagatatataattgtccacttttaatacaatttactgtgtgatattgacct---taacctttcacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG
                                                ||  || | | |      |||  |    | || | || ||| ||||     |   |  |||   | | || |   ||  |  |   |  | |||   |||||||||||| ||||||||||| ||||||||||  ||||| || ||||| || || ||||||
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG

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|27426102|gb|CA937622.1|CA937622
EST:     CTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAG                         CTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACA
genomic: CTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAGgttggtgact ... cacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACA
EST: gi|10233048|gb|BE801936.1|BE801936
EST:     CTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAG                         CTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACA
genomic: CTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAGgttggtgact ... cacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacttttaatacaatttactgtgtgatattgaccttaacctttcacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG
                                        cctttcacttc  CT-rich tract
     ttttaatacaatttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctgtgatgcatcttgattcattcagctatgagatatataattgtccacttttaatacaatttactgtgtgatattgaccttaacctttcacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA