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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtaaatttttccattaatagtttcactttgaccacgataaagctgccatgattagtttgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

Basic information

species Glycine max
transcript GLYMA12G03660.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
------tctgtaaatttttccattaatagtttcactttgaccacgataaagctgccatgattagtttgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
        |   |||  ||| |   ||| | || | ||   |  | ||||| | | |   | ||    |||     |||||        |   | |||    | ||||||||| ||||| |||||||| |||   |||||||||||||| || ||||||||||| || |||
aaattaaattccaatcattctacagataatatccccttcgacctg-taaagatccaactgt-agcccacttacatttttcacattgtttattgcactg----gcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
--tctgtaaatttttccattaatagtttcactttgaccacgataaagctgcca-tgattagtt-tgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
     ||    |      |  | |    |||   | | |   ||||||  |   |   |||     | |    || || | ||||   |   | |  ||   ||||||||| ||||| ||||||||||||   |||||||||||||| || |||||||| || || |||
aactagtggcataacttgtacacaaacccac---gcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacatttta-ctgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 4
tctgtaaatttttccattaatagtttcactt-tgaccacgataaagctgccatgattagtttgcttgggc--atttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
      | |    | |    |   |  ||    |   |  |||||||  |       |   |||     |  || |  | ||||   |   |   | | | ||||||||| || || ||||||||||||   |||||||||||||| || |||||||| || || |||
--aactagtggcacaacatgtgcgtgaacccacgggtagcataaagcctcaggttgcaagctgcacatccttatattttcacaatgcacatttcat-tggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG

upper sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 5
tctgtaaatttttccattaatagtttcactttgaccacgataaagctgccatgattagtttgcttgggcatttcatgacaaccaaatctctgt---cttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
   |    |||||   || | | | |  ||   || |  |    | | || |      |||      || ||  |||  ||  |  |     |   |||||||||||||| |||||||||||||||||   ||| || |||||||||||||| || |||||||| |||
-gagatgctttttgtgtttacaatatt-ctagaactataaatgtgat-ccctttcccttttcaacaagccttcaatgctaattacttgcaaatttgcttgtagATCTTCGAGATGATAAGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAG

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|298171505|gb|HO016537.1|HO016537
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|58014286|gb|CX701028.1|CX701028
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|58020948|gb|CX707690.1|CX707690
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|151401174|gb|EV270988.1|EV270988
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|151405308|gb|EV275122.1|EV275122
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|18039985|gb|BM308279.1|BM308279
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|308222701|gb|HO760611.1|HO760611
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAGGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|58021197|gb|CX707939.1|CX707939
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298170161|gb|HO018785.1|HO018785
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|192329144|gb|FK021131.1|FK021131
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298172850|gb|HO019834.1|HO019834
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgttagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccatgattagtttgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
                                         tctctgtctt  CT-rich tract
        attagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtaaatttttccattaatagtttcactttgaccacgataaagctgccatgattagtttgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

- - - - - - -ccattaa
- - - - - - - - - - - - - - - -tgaccac
- - - - - - - - - - - - - - - - - - - - - aagctgc
- - - - - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccaaa