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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

Basic information

species Glycine max
transcript GLYMA08G03570.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtg---tgcatgttcgat-taca--tttatgtgtgcat-tgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
    |||||||        | ||| || |    |   || ||||| |   |||  ||| ||  |||   ||| | | || || ||  ||         ||||       ||  ||   | || |      || |||||||||| || |||||||| ||| ||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| || ||||| || ||
----gtaaagatcttgtttt-tatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaagg-aggaaatcaagcattgca-tttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                |||  | |   ||  | ||     ||| |  ||  |       ||   |||||      |    |  |||   || | ||   | ||| |||||| ||||||| || || |||||||||||  ||||||||||||| || ||||| || |||||||| || || || || |||||| ||||||| || ||||| || ||
--------------------------------gtaactatgtttgctt-cacacaggataaggttgttacacatcttat-tactggtctctattgtactaagttgtgaagttccctattattatttg-cagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 12
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                   |  ||       |  || |    ||  |         || |||| |  |   |    | ||  ||   |   || || |  | |||||   ||||||| || || ||||| || ||  |||| |||||||| |||||||| ||||| ||||||||  | || || ||||  ||||||||||||||||| || ||
----------------------------------gtcagtcgcctcttttat-tctacttttagcatcccaagctttgcttgatttcact--gtaacaaaatctcagatcttatgcttctatt--gcagATCCTACATACATGATACGTGCCATTCCTAGCAATGCATCTGACAATGTGTATTGCACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaat--caagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                                      | | || | |   |||    ||| ||     | |   |  | |  ||  |||  ||  | ||| | ||| |   ||||||||||||| ||||| || ||  | ||||||||||||||||| ||||| || |||||||| || ||||| || |  || |||||||||||||| || ||
-------------------------------------------------gtcagtggttttcttcggtgt-catatttcagggccagaactgctagttacacacatctcagatgtttcttctact--gcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 12
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                           |  ||| || |||  |   ||  |||  ||| || |     |||  |     |||||  ||  ||  |  | |||   |    ||||||||||||| ||||| || ||  |||| ||||| || ||||| || || ||||||||||| || ||||| ||||  || |||||||||||||| || ||
------------------------------------------gtcagtg-attttctctggtatc-atgcttgctttacggcaagaattgctagcatcaaatatctcagatgctgttatcctactgcagATCCAACGTACATGATACGTGCCATTCCTAGCAACGCCTCTGATAATGTCTACTGCACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                           | |||  |   |   || |   ||| |      ||   | ||   ||   ||  ||||   |||| |||||       | |  ||||||| |||||||||||||| || |||||||||||||| |||||||| || || ||||||||||||||||||||||||||||||||||| |||||||| ||
------------------------------------------gtttgtatacactatctttctaatatatagaagctgggcaatggctggtctaa-ccaagtgctgcacttttt------gtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
--gttcgtaaagacaa---aaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
  |  | ||    ||    |||||| |   ||| | | | ||  | | || || |  || |   || ||| |||       |       |     |||   |  |  ||      |      |  |||   ||||||||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||  | |||||||| || ||  | |||||||| |||||||| ||
gtggccatatgcccagttgaaaacttttggttttttc-tttgc-tgcttg-gttctcgtgcttctatattcatgaaattccttttagtcgtttttagg--cttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------gttc-gtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcg--attacatttatgtgtgcattgcatactgaaaggaggaaatcaa--gcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                           |||  || | |   |       |     | ||| | |||  |  | |     |||  |  ||| | |  ||    ||   |   |  |  |    | | || |    | |||   || |   |   ||   ||||||| ||||||||||| |||||| |||||||||||||||| ||||| || ||||||||| | || ||||| || ||  | ||||| || |||||||| ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 12
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttac-tatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                        |||| ||   |  |||| |||   |  |||  | ||   ||  ||     ||      | ||| || | |  | || | ||| || |   |  |  | |||| ||||||||||||||||||| ||||| || || |||| ||| || || ||||| ||||||||  |  | || || |||||  | || || || ||||| |||| 
-----------------------cattt-tatcca-atgtaaatg---gtctgtgggcttttgttactgca-atataatccgccgaatgg-gaattttaatctttgaatgtacgtggatgtgtttggcagATCCAACGTATATGATTCGAGCTGTGCCTAGCATTGCATCGGATAACGTCTACTGCACTTTGTTGGCACATAGTGCCATCCACGGTGCTATGGCTGGTTT

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttga----cagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                                                      || || ||| |||      | |    ||  || ||   |||| | | |   |||||    |||||||||||||||||||||||||| | |  ||||| || || ||||| || |||||||| || || ||||| |||||  | || ||||| ||||| || ||
----------------------------------------------------------------------gt-cagtgcctac------gtgtttttcttgccttttcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

upper sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ23976 (Selaginella moellendorffii), 3'ss of exon 11
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttga----cagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                                                      || || ||| |||      |||    ||  || ||   |||| | | |   |||||    |||||||||||||||||||||||||| | |  ||||| || || ||||| || |||||||| || || ||||| |||||  | || ||||| ||||| || ||
----------------------------------------------------------------------gt-cagtgcctac------gagtttttcttgccttctcttttctctcaacttttgattttcagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA
                                  tttttttttactattt  CT-rich tract
                            attgcattttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtgtgcatgttcgattacatttatgtgtgcattgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

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