Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccctaagttctgttatgatcctttgttgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

Basic information

species Glycine max
transcript GLYMA13G23790.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 4
-tccctaagttctgttatgatcctttgt-tgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
 |  |  | |      |  ||  |  |  || ||    ||||  | |||   |    || | || ||     | | |     |     ||||  ||||  ||| ||| |||||||||| |||||||| || ||||| ||||||||||| |||||||| |||||||| || ||||||||||| |||||||| ||||| || ||
gtgtcctattgaaaaaaaaattataagaatgatgccg-tattaatatttctatcttgatcaatatttcctttagcatgaaaacctcattcttccttct-cagGATATGGTGGTGATGTCTGGTTCCCCCAACCAGCACCAAAGGATCACCCATGGCGATACATGCCTAATCATGCCATGACCCCTCATATCTCTGGGACTAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g29220.1 (Oryza sativa), 3'ss of exon 5
tccctaagttctgttatgatcctttgttgttgttac------tattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
     || || |   |  |   |||||       |       | ||        |  |  | |  ||   | ||  |        ||| ||| ||| | |    ||| ||| ||||||| || |||||||| |||||||| ||||||||||| |||||||| |||||||| || ||||| ||||| |||||    ||||| || ||
-----aaattattgaagaaaattttgtcagaaagaaaaagagtgttgtgcacctatgtaaattagctgtctctgaaagaacaaaccctcatc-cttgtgttgtcagGATATGGTGGTGACGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G049811_T01 (Zea mays), 3'ss of exon 4
-tccctaagttctgttatgatcctttgttgttgttactattcc-tttttaagttg-caattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
 | ||||  || | |    |   |  |    |  | | | |   ||  ||  ||| |   ||||   | |  |||      ||  | || |  |||||   ||| ||  |||||||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || ||
ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattccc--atttcc-cagGATACGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
-tccctaagttctgttatgatcctttgttgttgttactattcc-tttttaagttg-caattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
 | ||||  || | |    |   |  |    |  | | | |   ||  ||  ||| |   ||||   | |  |||      ||  | || |  ||||||  ||| ||| |||||||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || ||
ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattccc--atttct-cagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G418005_T01 (Zea mays), 3'ss of exon 3
-tccctaagttctgttatgatcctttgttgttgttactattcc-tttttaagttg-caattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
 | ||||  || | |    |   |  |    |  | | | |   ||  ||  ||| |   ||||   | |  |||      ||  | || |  ||||||  ||| ||| |||||||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||| | || ||
ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattccc--atttct-cagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTAGGACTAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G423972_T02 (Zea mays), 3'ss of exon 3
-tccctaagttctgttatgatcctttgttgttgttactattcc-tttttaagttg-caattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
 | ||||  || | |    |   |  |    |  | | | |   ||  ||  ||| ||  ||||   | |  |||      ||  | || |  ||||||  ||| ||| |||||||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||| | ||||| || ||||| || ||
ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgacaggtactttgtgtaacatggagcatctcattccc--atttct-cagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGGCCCCTCACATCTCTGGGACTAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G362021_T01 (Zea mays), 3'ss of exon 6
tccctaagttctgttatgatcctttgttgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC-------------
         ||  ||||  | ||     | |    | | |  |  ||  |||   |||  ||| |||    | | |  |  | | | |      || ||||  |         | |  |||||||| ||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || ||             
-----ggactcgtttatatttct--aacgctaacccgacttgtagttgtgtttatatttgtaaatttcagtttcgccctattcacccccc----ctctaggcgac--------tatcagGTTCCCATAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATATCTGGGACTACAATTGATGCGCAT

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 4
----tccctaagttctgttatgatcctttgtt--------gttgtt-actattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
    |   | ||  || ||  | | ||| | |        |||||| | | || |||||||   |||| ||   ||         | || ||   | | ||| ||||    |||||| ||||| ||||||||||  ||||||||||| || ||||| ||||||||||| |||||||||||||| || ||||| ||||||||||||||||||||
gtaatgtttcagcacttttgagtttcttggatttgagtatgttgttcaatgtttcttttta---tgcagttttgaaagccaatgacttcattttaattttctgattttc--agGTTACAGTGGGGATGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: PP1S106_16V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------tccctaagttctgttatgatcctttgttgttgttactat-----tcctttttaagttgcaattactaattttgccatc-ctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
                                           || ||||  |    |   |  |||  ||      |  ||      |  |    | | ||  |   |  |    | ||| ||    | |  |  |  |  |    ||| ||| | || ||||| |||  | | ||||| ||   |||||| ||||| |||||||||||||| ||||| |||||||| || ||||| || ||||| ||
gtaactcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcctaggcttgcttaccaggaacatgaacaccaatcacgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: EFJ13636 (Selaginella moellendorffii), 3'ss of exon 6
tccctaagttctgttatgatcctttgttgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
                               ||  || ||   || ||  || |   |  | ||||||      |   || |     |||  |    |||| ||  |||| |||||||||| ||| |||||  |||| || ||||| |||||||| | |||||||||| | || |||||||||||  | |||||  | ||
-------------------------------gtctctcttttcttctatttttctgctg-tgattttgt-----ttgatcttgggaacttgatc---tagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC

upper sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28931 (Selaginella moellendorffii), 3'ss of exon 7
tccctaagttctgttatgatcctttgttgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
                               ||  || ||   || ||   | |   |  | ||||||      |   || |     | |  |    |||| ||  |||| |||||||||| ||| |||||  |||| || ||||| |||||||| | |||||||||| | || |||||||||||  | |||||  | ||
-------------------------------gtctctcttttcttctattcttctgctg-tgattttgt-----ttgatcttgggaacgtgatc---tagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC

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|11275020|gb|BF325344.1|BF325344
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|17401257|gb|BM178039.1|BM178039
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|42723252|gb|CK769151.1|CK769151
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATGCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|214008422|gb|DB989988.1|DB989988
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|42723195|gb|CK769094.1|CK769094
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|4260047|gb|AI416543.1|AI416543
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|15199628|gb|BI423928.1|BI423928
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|6341426|gb|AW164250.1|AW164250
EST:     TGCAGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|18735405|gb|BM528746.1|BM528746
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|11688868|gb|BF596544.1|BF596544
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|7232927|gb|AW568278.1|AW568278
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTTCCACAGCCA
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCA
EST: gi|16995760|gb|BM085132.1|BM085132
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|209715917|gb|BW650930.1|BW650930
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|26060128|gb|CA803042.1|CA803042
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|13790807|gb|BG653398.1|BG653398
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGNTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCA
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATG-TTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCA
EST: gi|7232967|gb|AW568318.1|AW568318
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAA                         GTTATAGTGGTGATGTGTGGTTACCACAGCCAGCTCCTAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
EST: gi|6200999|gb|AW153099.1|AW153099
EST:     TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAG                         GTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT
genomic: TGCGGACACCCAAGCAATTGCAGATGCTTGCTCCAGTGGCCACGTTGCAGgtaattaacc ... atttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
                       ccatcctctttcctaa  CT-rich tract
         aattactaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccctaagttctgttatgatcctttgttgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC