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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtatatttttatatttatatatttttatgttcagaggtggaataatcgtattcagggaaaatgttctttgaaatttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG

Basic information

species Glycine max
transcript GLYMA11G06250.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 2
gttggtatatttttatatttatatatttttatgttcagaggtggaat--aatcgtattcagggaaaat--gttctttgaaatttcact-cagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
    |||  |    || || ||  |   | ||  ||         ||  |||  | | |||  |||||  ||||| |   || |  || ||||| |||||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| || |||| ||| || ||    |  |  || | ||| ||||
----gtaagtcaggatcttcatg-acgctcattctctagttcaccattcaatattttccagcaaaaataagttctctatcatgtatctacagGTTATTTTAACCCCAACTCATCTTGCTATTGTCATGGAATATGCCTCTGGTGGTGAGCTTTTCGAGAGAATTTGTAAGAATGTACGGTTCAGTGAAGATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 3
gttggtatatttttatatttatatatttttatgttcagaggtggaataatcgtattcagggaaaatgttctttgaaatttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
       |   ||   |||   ||  | ||     |     |   ||  |   |         | | ||||||| |         |||| ||||||||||| || ||||| || ||||| ||||||||||| ||||| || ||||| |||||||  || || ||    | ||  || | ||| ||||
------gtgagttgggattgtgatgctgtttctccccagaattccattgttaaacatttttttattcttctttgta----tgtctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGGATATGTAAGAACGTGCGATTCAGTGAAGATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 2
gttggtatatttttatatttatatatttttatgttcagaggtggaataatcgtattcagggaaaatgttctttgaaatttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
    ||   ||   ||  | ||    |||      ||||  |  | |  |   |  |     |||| ||||||| |     |   |||| ||||||||||| || ||||| || ||||| ||||||||||| ||||| || ||||| ||||||| ||| || ||    | ||  || | ||| ||||
----gtgagttgggattgtgatgctgtttctcccccagaattc-atttgttaaacacttttgaaat-ttctttgta----tatctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
----------gttggtatatttttatatttatatatttt-tatgttcagaggtgga--ataatcgtattcagggaaaatgttctttgaaatttcactc-agGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
          | |  | ||   | |   ||   |||| |   | ||   | |||||  |||     |||  |  |  |  ||| | |||||  ||||  ||||||| |||||||| || ||||| || ||||| |||||||||||  ||||||||||||| |||||    || ||||| |||||||  || | ||||||||
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaattt-gctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------gttggtatatttt---tatatttatatatttttatgtt---cagaggtggaata-atcg--tattcagggaaaatgttctttgaaatttcact----cagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
                                                        | ||| |   |   | | |  ||  | |||   | |   ||    ||||| | || |   ||| |||   | |     ||| | ||  |||    ||| |||| || || || || ||  |||||||||| |||||||||||  ||||||||||||| ||||||  ||| || || ||||  |  || | ||| ||||
gtgatcattctagactttttgattttttattattattaatttttttttccctgaacttgtagaccctgggtgtgtggatgaactttctggattgacattactggaagatattggacatttaggagtactaaagcttgtacttgaactatttcagATCATGTTGACTCCAACCCACTTGGCCATTGTGATGGAATATGCTGCTGGTGGAGAGCTGTTTGAGCGAATTTGTAAAGCAGTCCGGTTCAGTGAAGATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------gttggtatattttt---atatttatatatttttatgttcagaggtggaataatcgt-----attcagggaaaatgttctttgaa---atttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
                                      |||| || | |||   ||   || ||||| |    |     |||    |    ||     |||| ||     |     |||      ||||| ||||||||| || || || || ||| |||||||||| |||||||||||  | ||||||||||| ||||||  ||| || ||||| || |  || |  || ||||
gtgtgaaagaagcagctctttcgtattttgcagaggttttggaatctattttgcatggataaatattctggcatgacatggttagctccctgttacaaattctggagtgctaaatcttgtgctcgtttcattcagGTCATGTTGACCCCGACCCATTTGGCCATTGTGATGGAATATGCGGCGGGTGGAGAGCTGTTTGAGCGAATTTGTAATGCTGGTCGGTTCAGCGAAGATG

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|11412335|gb|BF424346.1|BF424346
EST:     CATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTNNTAAG-AG                         GTCATTNTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGG
genomic: CATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTT-TAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGG
EST: gi|22931738|gb|BU548877.1|BU548877
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|213618240|gb|DB973010.1|DB973010
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|9258485|gb|BE346632.1|BE346632
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|254317661|gb|GR826645.1|GR826645
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|14259137|gb|BG882045.1|BG882045
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|14259185|gb|BG882093.1|BG882093
EST:     CATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGG
genomic: CATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGG-AGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGG
EST: gi|19348943|gb|BM893475.1|BM893475
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|209714671|gb|BW674234.1|BW674234
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|7684855|gb|AW755503.1|AW755503
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTNTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|209697502|gb|BW670003.1|BW670003
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagaggtggaataatcgtattcagggaaaatgttctttgaaatttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
                                             tttcactc  CT-rich tract
                                      tttgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtatatttttatatttatatatttttatgttcagaggtggaataatcgtattcagggaaaatgttctttgaaatttcactcagGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG