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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatttattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA

Basic information

species Glycine max
transcript GLYMA02G01920.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
-tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatttattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA
 ||    |    ||| |  ||  | | | |  ||     | |  |     ||| ||   | |     | || |||||  | | ||      | | | | || | ||||| || ||||| ||  | || |||||||| || ||||| |||||||| || || ||||||||||| ||||| || ||||| || |||||||| 
attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtgc-agACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 4
-tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatttattt--tttgcctcttctttttaaaatatac-cagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA
 |||||| |  | ||     || ||||||      ||   ||  | | | || |   |||| ||||  | ||   |||  ||| |||| ||    | |   |||||  | || || |||||||| || || || ||| | ||||||||||||||||| |||||||||||  | |||||||| ||| |||| ||| |||| |||
ctttgacgtcatttt----gttatttaatccaaaattcatatactctattttctctgcagtcttaacattttaaatttatctcatcttattcggttttggacagTCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 6
tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatt--tattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA
  |  ||     | |     |   || |   |||  |     | |||    | |||| | | | | |  || || || ||     |   |    | |  |||||  | || |||||||||||||| || |||||| | ||||| ||||||||||| ||||||||||| || |||||||| ||| |||| ||| |||| |||
--tttctagacctcttcacattcctattgcatttgcacttgggctttatggtctatctgctctgaatcctaattctttccaaacttaccttgtttctggcagTCCTTCGAGTTCAAAGATATTGTGAAAATTGGAAGAACTCACACTCAAGATGCTACACCTTTGACACTAGGACAAGAATTTGGTGGCTATGCTACTCAA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 6
-tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatttattttttgcctcttctt-tttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA
    | || |||| |   |||  | ||||  |   |  |   ||      | |  |  | |  |  ||   | | || || | ||| |||    | | |||||| ||||| |||||||||||| | || ||||| || ||||| |||||||||||||| ||||||||| | || ||||||||||||||||||  |||||||
ggcagcctatgtaatatatttaatataatgaggactactaggtgacacaatataaa--aatcattcttgcctctatgactttgcttattttgttttttccagTCTATTGAGTTCAAAGATATTATTAAAATTGGGCGTACTCACACTCAAGATGCAACGCCTTTGACTTTGGGCCAAGAGTTTAGTGGGTATTATACACAA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 5
--tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaat-ttattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA
  |||   |      |   | | | |   ||    || |  |||| ||| || |  |||     |||| ||   |   |  |     ||||    | |  |||  || ||| || |  || ||||| |||||||| ||||||||||||||||||||    ||  | || || ||||||| ||||||||  ||    ||||| 
tgtttctttccaaggtggatatgcatc--ttcaagttcaatattgattt-gtctgaatcttgcgtaatattggctgacggtttgatattttggtttttggcagCAAAATGATTTTAGCGACATTGTTAAGATTGGTCGCACTCATACTCAAGATGCTGTTCCACTCACCCTCGGACAAGTGTTTAGTGCATACTGCACACAG

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|16279870|gb|BI943659.1|BI943659
EST:     CAAGACTAATTCCCAGCCTGAAAACCTTACATGGTACACTAAACTCAAAG                         TCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGAT
genomic: CAAGACTAATTCCCAGCCTGAAAACCTTACATGGTACACTAAACTCAAAGgtttgaattc ... aatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGAT
EST: gi|151409155|gb|EV278963.1|EV278963
EST:     CAAGACTAATTCCCAGCCTGAAAACCTTACATGGTACACTAAACTCAAAG                         TCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGAT
genomic: CAAGACTAATTCCCAGCCTGAAAACCTTACATGGTACACTAAACTCAAAGgtttgaattc ... aatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGAT
EST: gi|192322683|gb|FK015020.1|FK015020
EST:     AATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
genomic: AATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
EST: gi|192310776|gb|FK000290.1|FK000290
EST:     AATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
genomic: AATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
EST: gi|209717303|gb|BW659018.1|BW659018
EST:     AATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
genomic: AATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttttatcagttttaatttattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA
              ttttaat  putative branch site (score: 3)
              ttttaatttatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgactttgtatttagttttctttaattggtttttatcattgtttttgtttttatcagttttaatttattttttgcctcttctttttaaaatataccagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGGTATACTACACAA

- -gactttg