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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctcaattttttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG

Basic information

species Glycine max
transcript GLYMA20G23080.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 6
gtatttc-tcaattttttgtttccttgtgctgcatatgtatcatca-ctttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
||| ||  |   | |    |||  | ||      ||| ||| || | | | || ||    ||    |||   || || ||   | ||||||||||| || |||||||||||||||||||||||||||||  | || |||||| | |||||||| |||||||| |||||||||  ||||
gtacttaattgttataccattttatggtttatgttatatatgatgagcgtcattctaggttttaaaatttctttgat-gtgatttctgtagCCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 3'ss of exon 6
-----------------------------gtatttctcaatttttt------gtttccttgtgctgcat--------atgtatcatcactttatgctgtagttacgtattagatta-attgttgatgctgta--gCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
                               ||||  || | || |        |||  || | |||||        |||     |||| | ||  |||    || |   |  | | ||| |  |  |||||  |||||| || |||||||||||||||||||| || |||||| | || |||||| | |||||||| |||||||| ||||||||   ||||
gtatgtgttgccatttttattttaaatggacattttccattcttctcatacaagttcgatgagatgcatcaaccagtatgcgatttcacatcattttgtc-caacatgcaacttcacattatgcaatctgtacagCCTGAGGACTGGGATGATGAGGAAGATGGAGAATGGACAGCTCCAACCATTCCAAACCCTGAGTACAAGGGACCATGGAACCAAAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 6
gtatttctcaattttttgtttccttgtgctgca-tatgtatcat-cactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
         | || | || ||  ||||  || | | | ||||||    || ||    | | ||  ||     | || |||  ||  || ||||||| || ||||| ||||||||||||||||| |||||  ||||||||||| ||||||| || |||||||| ||||||||   ||||
-------gtacttatgtggttatttgttatgtagtttctatcatatgattaataacatgggtatataaattctaaaatgtccat--tgcagCCTGAGGACTGGGACGATGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAGGGACCATGGAAACAAAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 6
gtatttctcaattttttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
    | || |  |  || |||  || ||| |  | |||   |  |       | | |      ||| |  |  |   |      || ||||||| || |||||||| |||||||||||||| |||||  ||||||||||| ||||||| || ||||| || ||||||||   ||||
---gtacttatgtggttatttg-ttatgcggtctgtgtcgtaggatggataacagcatgggtttataaattctaaaatgtgcattgcagCCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatttctcaattttttgtt-tccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgt-agCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
    |||  | || | | |  |   |||      ||       |  || | | | ||| || |  |||   ||  ||||   | || | ||||||| || ||||||||||| |||||||||||||||||  |||| || ||  |||||||||| |||| |||   ||||||| | |||
---gttcatacttgtctataattgatgtaaaatctaaaatctcttgctgtgttccgtatttgctgattt--ttcgttgtcctttctcttagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttctcaattttttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
     | | ||||||||  || | | || |||| |   |       |||||   ||    | || ||   ||   |  |     | |||||||| || ||||||||||| |||||||||||||||||  ||||||||||| ||||||| || ||||| ||   ||||||| | |||
----gtttgaatttttttcttgcat-tgatgcaaaaccaaatctgatttat--cgtctcgaggttttgattttgatcctttgtttatagCCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 6
----------gtatttctcaattt--tttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtatta--gattaattg--ttgatg-ctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
            | ||   | ||   | || |   || |  |  | | | | ||| | || |||  | ||  || | |||  || ||||    || ||| |  ||||||||||||||||||||||||||||||||||| |||||||| || || || || |||||||| |||||||| ||||||||| | |||
gtaagtaattagaatttatagttcagtatggtaaattcttttata-aggaaccataatttcatgggg-agaaacttgttactgaataatcagctttatgaccctagCCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACACCTCCAACAATAGCTAACCCTGAGTACAAGGGACCATGGAAGCCCAAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 6
gtatttctcaattttttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
|||| | |  | |     ||    |        | |   |  |   ||| || | | || |   | || | | ||  |||    | ||||||||||||||||||||||||||||||||||| |||||| | || |||||||||||||| || |||||||| ||||||||| |||||
gtatattt--aatccaaattgtgattcaaaaggttttggttttagttttctgatttggtaattgactaaaattat--ttggaattatagCCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG

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|4289620|gb|AI437497.1|AI437497
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGG-ATGATG
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATG
EST: gi|298193745|gb|HO040393.1|HO040393
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|254340600|gb|GR850902.1|GR850902
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|13790097|gb|BG652688.1|BG652688
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGANTGAG-AAGATGGTGAGTGGACACCCCCTACCAT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGA-TGAGGAAGATGGTGAGTGGACACCCCCTACCAT
EST: gi|58021776|gb|CX708517.1|CX708517
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|192307920|gb|FK003068.1|FK003068
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|26268307|gb|CA819370.1|CA819370
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|22521717|gb|BU080528.1|BU080528
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|16997164|gb|BM086536.1|BM086536
EST:     CTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: CTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|18040353|gb|BM308647.1|BM308647
EST:     AGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: AGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|19934771|gb|BQ079801.1|BQ079801
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|24136456|gb|BU926966.1|BU926966
EST:     GGTTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|6718756|gb|AW306403.1|AW306403
EST:     GGGTATGATGACATCCCATAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGNGATGATGAGGAAGATGGTGAGTGGACACGCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|207707986|gb|GD689865.1|GD689865
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCC-TACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|192307919|gb|FK003067.1|FK003067
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|26047705|gb|CA784416.1|CA784416
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|208268672|gb|GE072089.1|GE072089
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|22524331|gb|BU083142.1|BU083142
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|15203979|gb|BI426756.1|BI426756
EST:     CTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
genomic: CTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATT
EST: gi|14990999|gb|BI316672.1|BI316672
EST:     GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAG                         CCTGAAGATTGGGATGATGAGGAAGA
genomic: GGGTATGATGACATCCCAAAAGAGCTCCCAGATCCTGAAGCCAAGAAGgtatttctca ... gatgctgtagCCTGAAGATTGGGATGATGAGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG
                             tattagattaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttctcaattttttgtttccttgtgctgcatatgtatcatcactttatgctgtagttacgtattagattaattgttgatgctgtagCCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG