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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgcaatgtttagttctgaaaagacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG

Basic information

species Glycine max
transcript GLYMA07G00420.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 2
--ttatgcaatgttta-gttctgaaa--agacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG
    ||    |||     || ||| |  ||| |  | |   || |  || ||||   ||    |  ||       |||| | |||  ||  || || |  ||||||| ||||||||||||||||||||||||||  | || |||| |||||| ||||||||| |  | || || || |||||||| || || || ||||| ||| 
aacgatatcgtgtgggtattatgagagcagaaatttttagtaattctatcaaac---atttggt--aaatctttctgtgttaattgatcaattgcaatctttcagGTGCACCCAGAAGGAAAATATGTTGTTGATGTCGATAAAAGTATTGATATTACAAAGCTCTCGCCTTCAACAAGAGTTGCTCTTCGAAATGACAGCTATA

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 2
-ttatgcaatgtt-tagttctgaaaagacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctg--atttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG
  | ||  |  || |  ||  |    |  |   || |     ||||  || |     ||||    | | |   |||||   |  ||  |  || | || ||||||| || |||||||| |||||||| || || ||||| ||||  ||||| ||||||||||| || || || || |||||||| || || || || || ||| 
gatctgtcacattgtcatttggttctgttagccctttttg--taatggaaatc--ctaaatttctgtttaccagtgctattaacttctcaatataattattcagGTACATCCAGAAGGCAAATATGTGGTGGATATTGATAAAAGCATTGATATTACAAAGATCACACCTTCAACAAGAGTTGCTCTTCGAAATGATAGCTATA

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 2
ttatgcaatgtttagttctgaaaagacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG
                         |   |||| |   ||||  |    || ||     | || ||   |     | |   || |  | |  || | ||||| || ||||| || || ||||||||||| |||||||||| ||| |||||||| || || |||||||| || |||||||| || || || || || ||||
-----------------------gtatgaatcttttttattatcatgtttgtatttctacgaacatagttgtcagtaaggcttacactcccattttccagGTTCATCCAGAGGGGAAGTATGTTGTTGATATTGACAAAAGTATAGACATTACGAAAATCACTCCATCAACGAGAGTTGCTCTTCGTAATGATAGCTATG

upper sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 2
-ttatgca-atgtttagttctgaaaagacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG
 || |     ||  ||  | |   |  || |    |  ||     ||    |   ||   ||  |  || || ||  |     ||| ||| |   | ||||||| || |||||||| || |||||||| || |||||||| || || || || |||||||| || ||||| |||||||||||  | || || || || ||||
gttgtctgtgtgggtacattttgtagaacccgatagcaaacagtgtatggttt--tcttgtctcatttctatggttattcaccttcttttccttgtgttcagGTACATCCAGAAGGGAAGTATGTTGTAGATATTGACAAGAACATAGATATCACAAAGATCACACCATCAACTAGAGTTGCTTTACGGAATGATAGCTATG

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|17401363|gb|BM178145.1|BM178145
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|213594416|gb|DB970010.1|DB970010
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|15285225|gb|BI469116.1|BI469116
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|37996482|gb|CF808071.1|CF808071
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|37997640|gb|CF809229.1|CF809229
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|19269340|gb|BM885596.1|BM885596
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|5509172|gb|AI855730.1|AI855730
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTTAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|6912974|gb|AW394562.1|AW394562
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|151403300|gb|EV273110.1|EV273110
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|213617885|gb|DB957366.1|DB957366
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|298197166|gb|HO041909.1|HO041909
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|18732952|gb|BM527342.1|BM527342
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|213599336|gb|DB972278.1|DB972278
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|298180890|gb|HO022329.1|HO022329
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGCTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|7588108|gb|AW703911.1|AW703911
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|37997219|gb|CF808808.1|CF808808
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|16281256|gb|BI944393.1|BI944393
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|7458604|gb|AW666054.1|AW666054
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|213587656|gb|DB971379.1|DB971379
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|213618287|gb|DB973057.1|DB973057
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|120534038|gb|EH262171.1|EH262171
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|24205256|gb|BU964509.1|BU964509
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|18039807|gb|BM308101.1|BM308101
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|7478542|gb|AW666307.1|AW666307
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|18041169|gb|BM309454.1|BM309454
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|37995944|gb|CF807533.1|CF807533
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|19052933|gb|BM731600.1|BM731600
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
EST: gi|37995965|gb|CF807554.1|CF807554
EST:     ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG                         GTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT
genomic: ATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAGgtcacctcat ... acttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG
                           tgctgat  putative branch site (score: 3)
                                 tttttcctttacactt  CT-rich tract
                              tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgcaatgtttagttctgaaaagacacatctgtcaaattaataaaactggatcaaatccaagatcaattgtgctgatttttcctttacacttcttcagGTCCACCCAGAAGGAAAATATGTTGTTGACATTGACAAAAATATTGACATTACAAAGATTACTCCATCCACTAGAGTTGCACTCCGCAACGACAGTTATG

-tatgcaa
- - - - - - - - - - - -agacaca
- - - - - - - - - - - - - - - tctgtca
- - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - caaatcc