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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcatgggaattattactctcttctgtcatttttttctgcccagtaattctgacacaaactaatcaatatcagtacca...

Basic information

species Glycine max
transcript GLYMA16G06850.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 9
----------------------------GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtg---tgcctctttccattcaattttcatgggaattattactctcttctgtcatttttttctgcccagta-attctgacacaaactaatcaatatcagtacca----------------------------
||| | || |||||||| |||||||| || || ||||| | ||||||||||||| | ||||||||||| ||||| | ||| | || |||| | | | ||| | | || | | | | || ||| || | | | | ||||| |
ATTTAATGAACTGTTGCTTCTTCTGCAGGTTTTCTGTTTGGTTGCAATGGAAAAGCCTGTCTCTCTTAAGCCTGAGCACATTAGAGATGAGAAAGTCAAGgtactttacctttctctattctctacatgtcaatactatattgcagcttgccaatactataatactaagagtattatgttttagtccgttt--ctttagtactaaataaaaccagttccctgttaatgccag

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcc--tctttccattcaattttcatgggaattattactctcttctgtcatttttttctgcccagtaattctgacacaaactaatcaatatcagtacca
||||||||| | ||||| ||||| |||||| | ||||| | |||||||| || ||||||||||||||||||||| | | || || | | | | ||| | || || || | ||| | | | | ||| | | ||| | | | |
GTTCTTTGCCTTGTTGCCATGGAGAAACCAATATCTCTTAAACCTGAGCATATCCGGGATGAGAAAGTGAAGgtgaacaaatacttttcttgaccactttttgccattctatctggttttcgttgcctcttttatctgaattcatatgattgagaacc-tcactgtttgatct-

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtg-----------------tgcctctttccattcaa-ttttcatgggaattattactctcttctgtcatttttttctgcccagtaattctgacacaaactaatcaatatcagtacca--------
||||||||| | || || ||||| |||||| | ||||| | || |||||||| ||||||||||||||||||||| | ||||| ||||| ||| | | | | | | ||||| | |||| | ||| | |||| | | | |||| | || || |
GTTCTTTGCCTTGTCGCCATGGAGAAACCAATCTCTCTTAAACCCGAGCACATCCGGGATGAGAAAGTGAAGgtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcatttt-cagccaattaatattaataacaactgactgatttcttaaatgaacttcag

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcatgggaattattactctcttctgtcatttttttctgcccagtaattctgacacaaactaatcaatatcagtacca-
|| |||||| ||||||| ||||| || || || ||||||| ||||||||||| || |||||||||||||||||| || | || | ||| | | || || | | ||| || | | | |||| || | || | | |||| | |
GTCCTTTGCCTGGTTGCCATGGAGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactttgatactct-ctcacataaaactcataggcaactgttttattttattatttactaaaaattttgttgacatcttctaataatcaaaataaa

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: PP1S222_130V6.3 (Physcomitrella patens), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcatgggaatta--ttactctcttctgtcattttt---ttctgcccagtaattctgacacaaactaatcaatatcagtacca
||||| || |||| || ||||| ||||| ||||||||||| |||||||| |||||||||| ||||| ||||| || | || |||| || |||| | || | | ||| || | ||||| | || | ||| ||
GTTCTGTGTCTGGTAGCCATGGAGAAACCTGTTTCTCTCAGCCCTGAGCATGTTCGGGATGAAAAAGTCAAGgtacgctgaatctttttgcatttgcaatacaattcacctgcttgcatgtgtggttcatcaattctgattattatacgtttcacggacag----------------

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: PP1S192_39V6.4 (Physcomitrella patens), 5'ss of exon 10
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtg-----cctctttccatt-----caattttcatgggaattattactctcttc-tgtcatttttttct------gcccagtaattctgacacaaactaatcaatatcagtacca------------------------------------------------------------
|||| || | | || |||||||||||| |||| ||||| |||||||| ||||||||||||||||| ||||| | || | | ||| |||| | | | | | | || | | | |||| |||| | | || ||| || | | | | ||| |
ATTCTGTGTCTTTTGGCCATGGAAAAACCAATTTCCCTCAGTCCTGAGCATATTCGGGATGAGAAAGTCAAGgtaaggataatctttctggatttgcagcaatacttgttgtaccaaatgcttcatacatttcatgttttcttattgtagttgtgtgattggtttgcatgaaactgctttccgatactaattaagcttcaccattacactttttaatttgtttcaggttgtgatgtttttggtggtcag

upper sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 10
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct--ttccattcaattttcatgggaattattactctcttctgtcatttttttctgc-ccagtaattctgacacaaactaat-caatatcagtacca------------------------------------------------------------------------------------------
|| || |||||||| || ||||| ||||||||||| || || || ||||||||||||||||||||||| |||||| | | | || | ||| | || ||| |||| ||| | | | | | | | || || || || | | | | || | |||
GTGCTGTGCTTGGTGGCCATGGAGAAACCAGTTTCACTAAGTCCGGAGCACATTCGGGATGAGAAAGTCAAGgtgcggttacagtccctgtgaatatggatttcaat--ttaccttctctagcaagtgctatatacacctttaggcttgccaaattgttgtatgaaatgaaaaccgcatcaagtataggttacaactagagcttttctaatctatataagaaagattatcctgacctgtcttcctgttctgttctataatgagcag

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|6566164|gb|AW233801.1|AW233801
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|15815763|gb|BI788038.1|BI788038
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|7925329|gb|AW831416.1|AW831416
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|58023690|gb|CX710431.1|CX710431
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTTGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|254331186|gb|GR843305.1|GR843305
EST:     AAAAACCAGTTTCTCTCAG-CCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTAT-AATGATGAT
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGAT
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|37995462|gb|CF807051.1|CF807051
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|15661712|gb|BI699083.1|BI699083
EST:     CAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: CAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|58020056|gb|CX706798.1|CX706798
EST:     TGAGCACATTCGGGATGAGAAAGTGAAG                         GTTC-TGAAATCAGTGCTCCCTATTAATGATGATGAGG-TGTTTC-TGGAC
genomic: TGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTG-AATCAGTGCTCCCTATTAATGATGATGAGGTTG-TTCTTGGAC
EST: gi|16348742|gb|BI974337.1|BI974337
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|37994622|gb|CF806296.1|CF806296
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
EST: gi|17519559|gb|BM188601.1|BM188601
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... gaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctctttccattcaattttcatgggaattattactctcttctgtcatttttttctgcccagtaattctgacacaaactaatcaatatcagtacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcttc