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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT

Basic information

species Glycine max
transcript GLYMA05G36620.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                          || |||||| |     || | | |  |     |  | |    | ||  |  ||  | |  | || | |  || |   ||   |||| ||  || | |||||||||||||||| |||||||| |||||||||||||| || ||||||||||| ||| |  | ||||| || |||||||||||| | || ||||| |||||
----------------------ttttaaactaatgacatgccttttgtagttagttggtcgtcttgattatc--tggatagtgcactgtgattcatat-ttgactgaactgtctcatctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgt-tattctatggaaatgaaattatataatctttcctta-aatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                    |      |  || |   ||  |  |||||    |  |  |  | | | ||| |  |  || ||  |  ||| |  || |     ||| |      ||| | ||| ||||||||||||||| ||||| || |||||||||||||| || ||||||||||| ||| |  | ||||| || |||||||||||| | || ||||| |||||
--------------------attgttgatatatttcatgcatgatctatcagcac-atttcctgtgagcttgcactgtaacttgcctatttatgactga-----gctgtatcacctcctcattc-agGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 4
gtgagtacttttatacacatacacacaagcta-atgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                        | ||| || |||   |  |  || ||    |    ||    |   || |  | |  ||     | | || || |  |   || |      ||  | ||| ||||||||| ||||| ||||| || ||||| |||||||| || ||||||||||| ||| |  | ||||| ||  ||||||||||| | || ||||| |||||
---------------------tttagaagttacatg---gacacact-tgcttttagtgttgagcacatttcctgtgagcttgcatatctatttctgacttgaactgtatcacctcttcattc-agGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------gtgagtactttta---tacac-atacacacaagctaatgtctgttattctatggaaatga---aattata-----taatctttccttaaatt---------tttccttttgttgctaatgtctgctattc--tgtt-tcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                      ||| |  ||||    | ||   |   ||  | | ||||  || ||| | |  | ||| |   ||  |||     |||  | |     |||          |||   | || || |  ||    |  ||   |||| |   ||   |||||||||||||||| || ||  | |||||||||||||| || ||||| ||||| |||||    ||||| || |||||||||||||  || ||||| |||||
gtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgccaatgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatgatctgcgcagGTGAGGACTTTGACCACAGGGTGATGGAGTACTTCATCAAGTTGATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtct-gctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                  |||  | |||||||||    || | |     |      |||      ||  ||  |||    | |  | ||| ||||||  | | | | || || |    ||   |||||||||||||||| || || || |||||||||||||| || || || ||||| |||||    ||||| || |||||||||||||  || ||||| |||||
----------------cgatattc-caagctaatcatagtcaataacatgtgtcagaatggagggattgtt--ttag---tgtgatgttggtgctaaccttttgttgttatgat----ctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGAAGAAGCACCAGAAGGACATCAGCAAGGACAACAAGGCTCTTGGTAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                        | |   | | |   |  | |   || |||   ||  |  |  |   | || ||||  |      |   |     |    ||  | |   |    | | |||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||| || |||||||||||||||||  |||| ||| |
------------------------atagaattacggtggcaaatgggtg-aaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttttctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
||||| | |||| |    |   |  |    | || | ||    ||| || | ||  ||  |   ||  || |   |      |  || |  ||   |||       |||  ||    | | | ||||||||| ||||| ||||| || ||||||||||| || || ||||| ||||| ||||| |||||||| || ||||||||||||||||| ||||| |||||
GTGAGGATTTTTTTCTCTACTGATGCTCTTTCATCTTTG---CTCTTTGCACATTGAAAGA---AAATTTACGAGAGGAAAGTTATTATACTGTGGATGCTCAAGGTTCAATTCTTTCCTGC-AGGTGAGGATTTTGACCAGAGGATTATGGAGTACTTTATCAAGTTGATTAAGAAGAAGCACGGAAAGGACATCAGCAAGGACAACAGAGCTCTTGGGAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcc-cctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                                                               || | |   |  |   || ||||||| || || |   ||   |       ||  ||  | ||||||||||||| ||||||||| | ||||| |||||||| ||  | |||||||| |||||    |||||||| |||||||||||| | || ||||| |||||
--------------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcc-cctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                                                               || | |   |  |   || ||||||| || || |   ||   |       ||  ||  | ||||||||||||| ||||||||| | ||||| |||||||| ||  | |||||||| |||||    |||||||| |||||||||||| | || |||||||||||
--------------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactgacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGCAAGCT

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|16278459|gb|BI942915.1|BI942915
EST:     TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAG                         GTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtactt ... ccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|193703473|gb|FK641417.1|FK641417
EST:     TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAG                         GTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtactt ... ccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|9987179|gb|BE661287.1|BE661287
EST:     TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAG                         GTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtactt ... ccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|298192507|gb|HO036589.1|HO036589
EST:     TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAG                         GTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtactt ... ccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|298188302|gb|HO034995.1|HO034995
EST:     AATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCCATCTTGGAG                         GTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: AATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACT-CATCTTGGAGgtgagtactt ... ccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
EST: gi|298186644|gb|HO037277.1|HO037277
EST:     TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAG                         GTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA
genomic: TAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtactt ... ccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT
                     tgctaat  putative branch site (score: 2)
                             tctgctattctgtttc  CT-rich tract
     aaatttttcctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAAGAAAAAGCATGGAAAGGATATTAGCAAGGACAACAGAGCACTTGGCAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT