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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacatgttctttgaatctttaaaagttctgaaggttaaaggaagtcatgaccttattgatgttaaccttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT

Basic information

species Glycine max
transcript GLYMA11G11510.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 7
gtacatacatgttctttgaatctttaaaagttctgaaggttaaaggaagtcatgacctt----attgatgttaa-----------ccttgca-tacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAA---AAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT
||   || || || ||    |   | | | |  | |      |||   ||||| |||||    ||| |   | |           ||||| | ||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||   |||||||||||||| ||| || || ||||| || |   
gttggtatatcttattcatgttactgagaatcgttact-cagaagtttgtcattaccttcattattaactgtgatatgtgttcccccttgtaatacagAACGTGAAGGCTGTCTTTGATGCGGCCATTAAGGTGGTTCTCCAGCCACCAAAGCAGAAGAAGAGAAAGAAGAGAAAGGCACAGAAAGCTTGTTCTATAT---

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------------------------------gtacatacatgttctttgaatctttaaaagttctgaaggttaaaggaagtcatgaccttattgatgttaaccttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT--
                                                                                                       ||   | |||       |   | |  |     | | || |  | ||  |      |||||      |  |  |  || ||||||||||| || ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| ||||||| |||   |||||||  ||||   ||| | |  
gtaaacgcttgaattcaattgtggcttctatgctcaatgtgatgtgttggctctgctttaaacaattatgtaacttttccctttgtattctagcttgcgcatctatgaagatgggtggccagagtatgtagtccatcatggctgcaagatttttgtgtcttatgacgcctttcggtctatgcagAATGTGAAAGCAGTTTTTGATGCTGCCATCAAGGTTGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAGAAAAA---ACAAAAGAACTGTGTTATTCTCTGA

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
--------------gtacatacatgttctttgaatctttaaaagttctgaaggttaaaggaagtcatgaccttat----tgatgttaaccttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT--
               ||  |  |     | |  ||  ||        ||  | |||||  |   |   | ||| |     | || |  | ||   | ||||||||||| || |||||||||||||| |||||||| ||||| ||||| || ||||||||||| ||||| | |||   |||||||  ||||  |||  | |  
ggtcacaacgtgtcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAAAAA---ACAAAAGAACTGTGTCATACTCTGA

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtacatacatgttctttgaatctttaaaagttctgaaggttaaaggaagtcatgaccttatt-gatgttaacct--tgcat------acagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT---
         ||    || ||  |   || | | | ||   | |   |      |  | | ||    || || ||||   |  |  || ||       ||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| || |||||||||||   ||||| ||||   ||||||  ||||  |||| | |   
tttctgtaggtgggaacttgcaccaagattatgtcaactatgtagtgcactgtgtcaattatttttttgtttgatggcgatttattgtattctattgcagAATGTGAAAGCAGTTTTTGATGCCGCCATAAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAA---GAAGAAAAAGAAGCAAAAGAACTGTGTCATTCTCTAAT

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ04304 (Selaginella moellendorffii), 3'ss of exon 6
gtacatacatgttctt-tgaatctttaaaagttctgaaggttaaa--ggaagtcatgaccttattgatgttaaccttgca-tacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT--
     | | | || |    ||    | ||  || |    | |     |   ||  | | | | ||        | |||   | |||||||| ||||| || |||||||| || |||||||| || ||||| || ||||||||||||||||| ||||  |||   |||||||||||| | ||  | |  
----gtccgtcttgtgacaaaggagtgaagctttttgctgctgtgttgtttgttctaaacctcttccaaaattctttgtgctccagAATGTAAAGGCAGTGTTTGATGCTGCGATCAAGGTGGTCCTCCAACCTCCAAAGCAGAAGAAAAAAAAGAAGAAG---CAAAAGGCCTGTACGATACTCTAG

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ16760 (Selaginella moellendorffii), 3'ss of exon 6
gtacatacatgttctt-tgaatctttaaaagttctgaaggttaaa--ggaagtcatgaccttattgatgttaaccttgca-tacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT---
     | | | || |    ||    | ||  || |    | |     |   ||  | | | | ||        | |||   | |||||||| ||||| || |||||||| || |||||||| || ||||| || ||||||||||||||||| ||||  |||   |||||||||||| | ||  | |   
----gtccgtcttgtgacaaaggagtgaagctttttgctgctgtgttgtttgttctaaacctcttccaaaattctttgtgctccagAATGTAAAGGCAGTGTTTGATGCTGCGATCAAGGTGGTCCTCCAACCTCCAAAGCAGAAGAAAAAAAAGAAGAAG---CAAAAGGCCTGTACGATACTCTAGA

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|8401737|gb|BE057371.1|BE057371
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|6847035|gb|AW349325.1|AW349325
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|16996922|gb|BM086294.1|BM086294
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCT
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCT
EST: gi|193681399|gb|FK623261.1|FK623261
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTTAGTTCTCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGT-AGTTCTCCA
EST: gi|5760314|gb|AI965741.1|AI965741
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|151394170|gb|EV264041.1|EV264041
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|298177328|gb|HO027109.1|HO027109
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCAT
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCAT
EST: gi|26058249|gb|CA801163.1|CA801163
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|193642127|gb|FK589733.1|FK589733
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|298178107|gb|HO027490.1|HO027490
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|193727893|gb|FK665559.1|FK665559
EST:     AGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|193350327|gb|FK315329.1|FK315329
EST:     AGCTTATCGGTGCTCCAGTTTACATTGAATGTAGTTCAAAAACGCAACAG                         AATGTGAAGGCTGTTTTTG
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTG
EST: gi|192329017|gb|FK021091.1|FK021091
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAG-TAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|192297529|gb|FG989535.1|FG989535
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAAGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|7589250|gb|AW705028.1|AW705028
EST:     GCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAAG                         A-TGTGAAGGCTGGTGTTGATGCAGCCATC
genomic: GCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACA-Ggtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATC
EST: gi|208324913|gb|GE124839.1|GE124839
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAACCACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
EST: gi|192329018|gb|FK021092.1|FK021092
EST:     AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAG                         AATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA
genomic: AGCTTATCGGTGCTCCAATTTACATTGAATGTAGTTCAAAAACACAACAGgtacatacat ... ttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttctgaaggttaaaggaagtcatgaccttattgatgttaaccttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT
                                     tgttaac  putative branch site (score: 2)
                              ttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacatgttctttgaatctttaaaagttctgaaggttaaaggaagtcatgaccttattgatgttaaccttgcatacagAATGTGAAGGCTGTTTTTGATGCAGCCATCAAGGTAGTTCTCCAGCCCCCAAAGCAGAAGAAAAAGAAGAGAAAGGGACAAAAGGCCTGTTCCATTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA