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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat...

Basic information

species Glycine max
transcript GLYMA08G17000.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttattgattttat-ttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat----
||| |||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||| |||||||| |||||||||| |||||||||||| || ||| | | || || | | |||| | || | | | | | | | | || | || | | || |
GAGCAGGACATCCAGATGATGCTCGCCGCGGACGTCCACCTCGGCACCAAGAACTGCGACTTCCAGATGGAGCGCTACGTCTACAAGCGCCGCACTGACGgtaccgatctga-----aaccccccccctctgcctgcattatactcagatactcttgtgtacgatcgtcggctaccggtagatctgttcgtgttgttgatttgat

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g08440.2 (Oryza sativa), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgc---tccattctcaatttt--tcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat
||| |||| | ||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||||| |||||||||| |||||||| ||| | || | | | | | | | || | ||| | | | | | | | |||| | | | | |
GAGCAGGACGTGCAGATGATGCTCGCCGCCGACGTCCACCTCGGCACCAAGAACTGCGACTTCCAGATGGAGCGCTACGTCTACAAGCGCCGCTCCGATGgtacgcatgcacccacccccacctacaggcatctcacccggctctgcttgttcgtcgatgctcacagct--agccattacaatgttcttgccatgagatttc---

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G159237_T02 (Zea mays), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttatt--gattttatttttgaaagaatgatttcctttgcat-tgttcatag---tgttt-tattttttacaatggaat
||| ||||||||||||||||||||||||||| || |||||||||||||| ||||||||||| ||| |||| |||||||| | |||||||||||| |||||| ||| || ||| |||| || || || | || | || | || || || | | ||| || | | || | | || | |
GAGCAGGACATCCAGATGATGCTCGCCGCCGATGTCCACCTCGGCACCAAGAACTGCGACTTCCAGGTGGAGCGCTACGTGTACAAGCGCCGCACTGATGgta------ccaatccaaatctttcgagactaaccaaatgtttacctccaatgcttgttgtctttgatatctagttttagatctgctcgtgttgacttctattgga-

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G126821_T01 (Zea mays), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgc-tccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat-
||| |||||| ||||||||||||||||||||||| ||||| |||||||| |||||||| || |||||||| ||||| | ||| |||||||||||||| ||| ||||| | | |||| | ||| | | | | || | | | | | | || ||| | | | | |
GAGCAGGACATACAGATGATGCTCGCCGCCGACGTCCACCTTGGCACCAAGAACTGCGATTTCCAGATGGAGCGCTATGCCTTTAAGCGCCGCACCGACGgtatctgccttcgctctcgcatccgtgcctttttcctatccgtatgccaatacacg--tagatgtagactgaaaataaaccaatcgctcgtgcccaagtgct

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G092719_T01 (Zea mays), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgc-tccattctcaattt-ttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat
||| |||||| ||||||||||||||||||||||| ||||| |||||||| |||||||| || |||| ||| ||||| ||||| || ||||||||||| ||| | ||| | | || || |||| ||| | ||| | ||| | || | ||| | | | ||| |
GAGCAGGACATACAGATGATGCTCGCCGCCGACGTCCACCTTGGCACCAAGAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgccttcgctcctgcttccttccccttttcttttttcctccgcatgccaatccatgtagatgtaggtgctccagtagaccagtact-acagttctg-

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G145308_T01 (Zea mays), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttt-tattttttacaatggaat
||| |||||| |||||||||||||| |||||||| ||||||||||| || |||||||| || |||||||| |||||||| || ||||| |||||||| ||| || ||| | | | | || |||| || | | || | | | | | || |
GAGCAGGACATACAGATGATGCTCGCTGCCGACGTCCACCTCGGCACTAAGAACTGCGATTTCCAGATGGAGCGCTACGTTTTTAAGCGACGCACCGACGgtacgtgtcttcttcactcccgcatccctgcctccccccccttcgcatgcgaatcatgtagatgacagcaaggaggccgctggtgcccagtgttatagtt-

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G099657_T01 (Zea mays), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctca-atttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat
||| |||||| |||||||||||||| |||||||| |||||||||||||| |||||||| || |||||||| || || ||||| ||||| |||||||| ||| | | || || | || | | |||| | | ||| ||| || || | | | | | |
GAGCAGGACATACAGATGATGCTCGCGGCCGACGTCCACCTCGGCACCAAGAACTGCGATTTCCAGATGGAGCGGTATGTCTTTAAGCGTCGCACCGACGgtatgttctttcctcccgcatcccttcctttttgcctctccgcatgcgaatccatgtagatgttgacaggaaggaggccgctggcgctccagtgttacag-

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G099657_T03 (Zea mays), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACT---TTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctt---tgcattgttcatagtgttttattttttaca-atggaat---------------------
||||| | || | | || | | | | || | | | | || | | ||| || | | | | | | || ||| |||| | ||| | | | | | | | | || ||| | | | |||| |||
-------------------------GCGCCGCCACTC--CCTGACATCGAGACCGGCTGCCCGACCCCGGTCCGGCGATCCCTCTGCACCCCTTTCTTTG-CGCTGCCAGCCCCAATCTCTCGCATCCctgtcaaccatggcggcgtcagcaggcggaggcgcggtgcgcgcgctgtcccagaaggagcaggacatacagatgatgctcgcggccgacgtccacctcg

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G04770.1 (Arabidopsis thaliana), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtct-ctgctccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctttgcatt-gttcata-gtgttttatttttt-acaatggaat
|| | || |||||||||||| | | ||||| |||||||| || |||||||||||| ||| ||||||||| || || |||||||| | ||| ||| ||| || ||| ||| | || | || | ||| | | |||| | | |||| | | | || ||| || | | |
GAAGCTGATATCCAGATGATGTTATCAGCCGATGTTCACCTTGGTACCAAAAACTGCAACTATCAGATGGAGCGTTATGTCTTCAAAAGACGCGACGACGgtaaactatctcatcttcatccaaatttcattgtacatgtaattctatatagaagcaacgtttccacattcatctacacgtagcttacgaattgatagtt----

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgt-ctctgctccattc-----tcaatttttcctttttattgattttatttttgaaagaatgatttc-ctttgcattgttcatagtgttttattttttacaatggaat
|| |||||| |||||||||||||||||||| ||||||||||| ||||| ||||| |||| ||||||||||| ||||||||||||||||||| |||||| |||| | || ||||||| || || | | | || || | |||||| || | | | || ||| |||| |
GAACAGGACATACAGATGATGCTCGCCGCCGAGGTTCACCTCGGTACCAAGAACTGTAACTTCCAGATGGAACGTTACGTCTTCAAGCGCCGCAATGATGgtactctatctctctcattcttcaatttcctgttgaaatctttcgtctcttcgattgggtgatttttctctttgtcgatctgcatgtgcatttttctttc-------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S173_16V6.1 (Physcomitrella patens), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgt-----ctctgctccattctcaatttttcct----------ttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat------------------------------------------------------------------------------------
|||| || | ||||||||||| || || || || |||||||||||||| ||||||||||| |||||||| |||||||| | ||||| ||| |||||||| ||||| || | | ||| |||| | |||| | | | || | || |||| | || | ||| | || | | | | |
GAGAGCGATGTGCAGATGATGCTGGCTGCTGATGTGCACCTCGGCACCAAGAACTGCGACTTCCAGATGGAGCGCTACGTGTGGAAGCGGCGCTCCGATGgtgagaactctgtcccctccattgtttgtcctcgtcccggtgtgttatcggtgtgggcttggggtgagaagtttctgtgttatgaatgataagggttcggggtgaagatacaagtttttttttggacgtgtgtatatgttttggacgggtcgtggtttggggtggttgactattgtggcttggcgggtccgttgcgcag

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S209_48V6.1 (Physcomitrella patens), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctct---gctccattctcaatttttccttttta----ttgattttatttttgaaagaatgatt-tcctttgcattgttcatagtgttttattttttaca---atggaat---------------------------------------------------------------
|||| || | ||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||| |||||||||| ||||||||| |||||||| | ||| | | | | || | || ||| || | || || || | | |||| | | | ||| |||||||
GAGAGCGATGTGCAGATGATGCTGGCTGCCGACGTGCACCTCGGCACCAAGAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGATGgtaattagggctttttccccctgtggcccgtgttggggtttggttgggtgcgtgtgcgagtgttcgttttttggtgcgggggcggcgcggggggtttggtgcggatggaattggtttgtgaaggtgggcgattgacgagggtagtggggtcgttgttttattctgtgtgggcag

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S59_133V6.1 (Physcomitrella patens), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattt--tttacaatggaat--------------------------------------------------------------------------------------------
||| | || | || |||||||| || ||||| || || ||||||||||| |||||||| || |||||||| || ||||||| ||||||||| |||||||| | || | || |||||| | || || || || || | | |||| | || || ||||| | |
GAGTCCGATGTGCAAATGATGCTGGCTGCCGATGTGCATCTCGGCACCAAGAACTGCGATTTCCAGATGGAGCGATACGTCTGGAAGCGCCGCTCCGATGgtattaattctcattagggttattccttag-acaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacag

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S48_103V6.1 (Physcomitrella patens), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttccttttta----ttgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat-------------------------------------------------------------
|||| || | ||||||||||| || |||||||| ||||| |||||||| ||||||||||| |||||||| |||||||||| ||||||||| | |||||| | || | | | | || ||| || | ||| | || | |||| | | | | || | | | |
GAGAGCGATGTGCAGATGATGCTGGCTGCCGACGTGCACCTAGGCACCAAGAACTGCGACTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCTGATGgtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcag

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ20712 (Selaginella moellendorffii), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgt----ctctgctccattctca--atttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat
|| | ||||||||||||||||| ||| | | ||| || || |||||||| |||||||| || |||||||| |||||||||| ||||||||| |||| ||| || || ||||| || || |||| | ||
GAAGCCGACATCCAGATGATGCTGGCCTCGGCCGTGCATCTGGGCACCAAGAACTGCGATTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGACGgtaagatcctagtcgcttctcgcgatcttagctttgtggtgccacag-----------------------------------------------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ32709 (Selaginella moellendorffii), 5'ss of exon 1
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgt----ctctgctccattctca--atttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat
|| | ||||||||||||||||| ||| | | || || || |||||||| |||||||| || |||||||| |||||||||| ||||||||| |||| ||| || || ||||| || || |||| | ||
GAAGCCGACATCCAGATGATGCTGGCCTCGGCAGTGCATCTGGGCACCAAGAACTGCGATTTCCAGATGGAGCGCTACGTCTGGAAGCGCCGCTCCGACGgtaagatcctagtcgcttctcgcgatcttagctttgtggtgccacag-----------------------------------------------------------

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|10847312|gb|BF070017.1|BF070017
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|24205688|gb|BU964941.1|BU964941
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|37996268|gb|CF807857.1|CF807857
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|22541501|gb|BU091344.1|BU091344
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|7232750|gb|AW568103.1|AW568103
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|298194300|gb|HO040948.1|HO040948
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|151405528|gb|EV275342.1|EV275342
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
EST: gi|22540179|gb|BU090022.1|BU090022
EST:     AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATG                         GTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG
genomic: AAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctc ... tttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACGGACATCCAGATGATGCTCGCCGCCGACGTTCACCTCGGCACCAAAAACTGCGACTTTCAGATGGAACGCTACGTCTTCAAGCGCCGCACCGATGgtctctgctccattctcaatttttcctttttattgattttatttttgaaagaatgatttcctttgcattgttcatagtgttttattttttacaatggaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA