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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagct-ctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag
||||||||| || || |||||||| || |||||||| ||||||||| | |||||||||||||| ||||| |||||||| || |||||||| || |||| || | | || | | | | | | ||||| |||||| | | | | || | | || || ||||| || ||| | | | || |
AATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCACAAGACAAgtaa---gaacaaaaacctggtttc--cctattcctttagctcctagattttacatcatatgaatggacgacttcctttattcatgaaatggaaaaaattgatta----------

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag
||||||||| || || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| || ||||| | ||||| || || |||| || | | || | | || | | | | || || ||| ||| || | || | | | ||| ||||| || ||| || || |||
AATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCACAAGACAAgtaa-gtcaac--ttacttgacggtcatctgctacctttctgatgaa------tcattaaacaagcagtcaagttctta--cttgatctatattttggagactcatgataa---

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag
||||||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| |||||||| || ||||| || || |||| || | | | | || | ||| | |||| | | || | | | || | | | | ||| | | | || | | |||| | ||
AATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCACCAGACAAgtaa--------gtaaacttgcatgaa---atttctgtagccaactatgaaccttatcatatattaactttgtccatcaatggtcaa-tcaagcacttgaactttgaattga--

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatc-ttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatct-tgagcttaattatgttttcttttgactgcag
||||||||| || || |||||||| || |||||||| || |||||| | |||||||||||||| ||||| |||||||| || ||||| || || |||| |||| | | | | || | | || ||| || | ||| | | | | || | || | | || | | | | | | ||||
AATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCACAAGACAAgtgagcaatctgttctctgctcatcagggtcatgtcttttgct-------gttcttttt----ttttgtgtgttcatatactgtatgcattccactttctaaatctctgac-----

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag
||||| |||||||| || ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||||||| | || || ||||| || ||||||| | | | | ||| | | | | || | | || || | ||| | | || ||| | | || | | ||||||||
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaa-----cccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaat----acttttgttttcgttatgtggactgcag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacat---ggacgatgatttcat-attatcttattcttt-----tagcgaggaa-aagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag
|||| ||||| || || || || |||||||| || ||||| ||||| ||||| || ||||||||||||||||| || ||||| || || ||||| ||||||| | ||| | || ||| ||| | || ||| | |||| || |||| | ||| | ||| | ||| | |||| | | ||| | | ||||| |
GATGAGTCCAGAGGATGATGCAGAGGAAGATGGAGCGAATATCGATCTGGACTCTCAGAGGAAGGGAAAGTGTGTCGTTCTAAAAACATCAACTCGTCAGgtgaagttttagactcttatatcaccgttagagagattttcagaactagtggggaacaaactctgactactagtgta-gtgtttgtataatgatctcatgggttaattatacttttcag-----

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattat-cttattctt----ttagcgaggaaaagctc-tcagtacaatag-tacatatttctttaatcttgagcttaattatgttttcttttgactgcag
|||||||||||| || || || || ||||||||||| ||||||||||||||||| || ||||||||||| |||||||| | || || ||||| || ||||| ||| | | | || || | | | ||| || | ||| | || | | | || || | | |||| | || || ||
AATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgt-acaccagcattttctcattaacatacatgtacttgtcttttacaaggtagagttaattggagcagtaaatggaattttcgaggacctgcagagcaaaa--------------------

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 3
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtga----catggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag
| || |||||||| ||||||||||| |||||||| ||| ||||| | ||||| ||||||| ||||||||||| || | ||||| || || || || || | || || ||| | | | | |||| | | || ||| || | || |||| | | || ||| || | |||| || || | |||
CGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgtaagttatatccacattgagattctctggcagtgacgtttt--ccacatgtgactgtcaatatgaattta---atttatatcatgttgcact-gacatcatttttttgtgtgtacag

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|6482551|gb|AW201806.1|AW201806
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|6915777|gb|AW397307.1|AW397307
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|298171738|gb|HO021330.1|HO021330
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGAC
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGAC
EST: gi|298167852|gb|HO013115.1|HO013115
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|254339477|gb|GR848235.1|GR848235
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTGGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|4313874|gb|AI460993.1|AI460993
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|33390542|gb|CA853737.1|CA853737
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACC
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACC
EST: gi|298195561|gb|HO043952.1|HO043952
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGA
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGA
EST: gi|209719376|gb|BW674456.1|BW674456
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|120530681|gb|EH258814.1|EH258814
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|7924448|gb|AW830474.1|AW830474
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|27427306|gb|CA938826.1|CA938826
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|18040691|gb|BM308985.1|BM308985
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|213598762|gb|DB968233.1|DB968233
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
EST: gi|7042249|gb|AW472143.1|AW472143
EST:     ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAG                         ACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT
genomic: ACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatgga ... ttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGAACCCAGAAGACGAAGCTGAAGAAGATGGTGCCAATATTGATCTTGACTCACAAAGGAAGGGAAAGTGTGTTGTGCTAAAGACTTCTACTCGACAGgtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA