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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA

Basic information

species Glycine max
transcript GLYMA05G36050.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaagg-aggaaatcaagcattgcattttttt--tactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                     || |||   |   |   ||     ||| |  ||  |  |    ||   |||||      |    |  |||   || | ||   |  || |||||| ||||||| || || |||||||||||| ||||||||||||| || ||||| || |||||||| || || || || |||||| ||||||| || ||||| || ||
-------------------gtaactatgtttgctt---cacacaggataaggttgttacacatcttat-tactggtctctattgtactaagttgtgaagttccctattattatttg-cagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
-----------gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttga--ttata-tttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactatt--tgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
           |||  ||| |   || | |  |   | | |   | ||||  ||||||  |  || ||| | |||| ||   |   |      | | |||   ||| |       | ||| |  |  || |||||||||| || |||||||| ||  ||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| || ||||| || ||
gtaaagatcttgttt-ttatgttcaattctcgatgcacatgcg-gagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaat--caagcattgcattt-tttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                                        |   || || | ||         ||| ||     | |   |  | |  ||  |||  ||  | ||| | ||| |   ||||||||||||| ||||| || ||  | ||||||||||||||||| ||||| || |||||||| || ||||| || |  || |||||||| ||||| || ||
---------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcat-tttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                                 ||  |    |||   |    | |||  ||| || |     |||  |     |||||  ||  ||  |  | |||   |    ||||||||||||| ||||| || ||  |||| ||||| || ||||| || || ||||||||||| || ||||| ||||  || |||||||| ||||| || ||
---------------------------------gtcagtgattttctctggtatcatgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 12
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                     |   ||  |||  | |  || |||| |   ||| || ||    |  || | |   ||   |   |    ||    || ||   |   | ||| ||||||| || || ||| |||| ||| ||||||||||||| || ||||| || ||||| |||||||| || || |||||| | ||||| || ||||| || ||
-------------------gtagccatttgtaactct-tatttttgct---attgatatagttgtaacacatttctagattggtctgtgaca----atattccatcggaattggcagATCCTACATACATGGTCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTAGCCCACAGTGCTATCCATGGTGCAATGGCGGGGTA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                             || ||| | ||   |   |   || |||  | ||  ||   | ||   ||   ||  ||||   |||| |||||      | |  ||||||| |||||||||||||| ||||||||||||||||| |||||||| || || ||||||||||||||||||||||||||||||||||| |||||||| ||
-----------------------------gtttgtatacactatctttctaatatatagaagc--tgggcaatggctggtctaa-ccaagtgctgcacttttt-----gtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
--gttcgttaagacaaactatacaattatacgtatgtgtgca-tgtttgatt---atatttatgtatgcattgcatactgaaaggaggaaatcaagcatt-------gcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
  |  | | | | | |  |  | | || |   | | | |    || ||| ||    |  || | ||| |||   || |      |  |   | | || |        | | |      |  |||   ||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
gtggccat-atgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------gttcgttaagacaaactata-----caattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaa--ggaggaaatcaagcattgcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                                          | |||         ||| |     | ||| |    |  ||||     ||| ||| |||  ||    | |  |||  |||    | |    || |  |    |||| |    |   ||   ||||||| ||||||||||| |||||  |||||||||||||||| ||||| || ||||||||| | || ||||| || ||  | ||||| || |||||||| ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacac-tgtggggaattgcttacattc-tggccacgtc-catggtgatcttgcattcgataagactgctcattatgcc-atagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 12
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactat--ttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                 ||   ||   | |||  || |  |||  | || | ||  || |   ||      | ||| || | |  | || | ||| || |   |   | |  ||| ||||||||||||||||||| |||||||| || |||| ||| || || ||||| ||||||||  |  | || || |||||  | || || || ||||| |||| 
----------------cattttatccaatgtaaatg-gtctgtgggcttttgttactgca-atataatccgccgaatgg-gaattttaatctttgaatgtacgtggatgtgtttggcagATCCAACGTATATGATTCGAGCTGTGCCTAGCATTGCATCGGATAACGTCTACTGCACTTTGTTGGCACATAGTGCCATCCACGGTGCTATGGCTGGTTT

upper sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ23976 (Selaginella moellendorffii), 3'ss of exon 11
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcatttttttt-actatttga----cagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                                                              || ||| |||      |||    ||  || ||   |||| | | |   |||||    |||||||||||||||||||||||||  | |  ||||| || || ||||| || |||||||| || || ||||| |||||  | || ||||| ||||| || ||
------------------------------------------------------------gtcagtgcctac------gagtttttcttgccttctcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgcatactgaaaggaggaaatcaagcattgcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA
                                   ttttttttactattt  CT-rich tract
                             attgcattttttttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttgattatatttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactatttgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA