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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG

Basic information

species Glycine max
transcript GLYMA05G21370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g39960.2 (Oryza sativa), 3'ss of exon 1
----------------------------------------gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgttt-gtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
                                        |   | |       |||   |    | | | |     |  || || |   ||  | ||||     | || |  |  |||   | | |||| ||||||||||||||||| || |||||||| || ||||| |||||||| || | |||||| ||||||||||||| ||| ||||||||||||
gtaaggagctcgccgcttccggatccaccctagccgccgcggcggcggcggccgcttcggcgtcttcttcttctccgctcaatctcccggttagtcccttctgattggtttcctcctttccctcgcagACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g60790.1 (Oryza sativa), 3'ss of exon 1
gttcgagatctgtt--cttattctcggtttccgtaattccataaccttcttcttctttc--cttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
  |   |   || |  | ||| ||      |    ||| | |  |    |||  |  |   ||    |||| | ||| ||  |    | |||| ||||||||| | || || || |||||||| ||||| || ||||| ||||| | |||||| ||||||||||||| ||| ||||||||||||
-gtaaggccttgcttccctatgcttaacgccta-gattgctttgcgggattcagcgctgaactgacctctcttcttgctgcatcggcgcagACCTTCAAGCGCCGCAATGGCGGCCGCAACAAGCACGGTCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899149_T02 (Zea mays), 3'ss of exon 1
gttcgagatctgttctt-attctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG-------
        |  ||||||      |  | ||| |  |  |     | |   | |||  ||||   | | || | ||||       | |||| |||||||| ||||| || || |||||||| ||||| || ||||| ||||| | |||||| ||||||||||||| ||| ||||||||||||       
-------gtgagttcttcgagaccaatctccct--tctcgccgacgttgccgtctaacctttgttgttgtctggttgccg--ccgcagACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGGTAACAC

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899149_T01 (Zea mays), 3'ss of exon 1
gttcgagatctgttctt-attctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
        |  ||||||      |  | ||| |  |  |     | |   | |||  ||||   | | || | ||||       | |||| |||||||| ||||| || || |||||||| ||||| || ||||| ||||| | |||||| ||||||||||||| ||| ||||||||||||
-------gtgagttcttcgagaccaatctccct--tctcgccgacgttgccgtctaacctttgttgttgtctggttgccg--ccgcagACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G129015_T02 (Zea mays), 3'ss of exon 1
gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtt--tgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
||  |  ||| |     ||   ||   ||||| |  ||    |     |  | | |       |||  | ||| |  | |||   | |||| |||||||| |||||||| || |||||||| ||||| || ||||| ||||| | ||| || ||||||||||||| ||| ||||| || |||
gtgagctatcggagaccatctccgtcctccgtcacgcctcgccgccgctgctgtctaaccctttcttttgttggttgtggttgccgcagACGTTCAAGCGGAGGAACGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATACGCTGCTCCAACTGCGCCAAGTGCTGTCCAAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G827266_T03 (Zea mays), 3'ss of exon 1
---------------gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
               |   ||  |  | ||||  || | ||    |||  ||   || ||  | | | || |              |||| | | |  | |||| ||||||||| | ||||| || |||||||| || ||||| || || ||||| | |||||| ||||| ||||||| ||| ||||||||||||
gcgagtcctaaccaagcctgaagttcgatcttcctccctgtgcatgtacatctcgaatctaatccattttactcc----------ctgttctctctccgcagACCTTCAAGCGCCGCAACGGCGGCCGCAACAAGCATGGCCGCGGTCACGTCAAGTACATCCGGTGCTCAAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgagatctgttcttattc-tcggtttcc-gtaattccataaccttcttcttctttccttga--atctcgtattgttgtttgt-ttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
          |  ||| |||| |||||| |   |  ||  || ||  |     |      ||||  ||||   |||||||||||| ||| |||| |||||||| |||||||| ||  | ||||| |||  | | || || |||||    ||| |||||||||||||||||||||||||||| |||
---------gtactctcattcatcggttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 3'ss of exon 1
gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
||  |   |   |    | | ||  ||| |    || | |    |  ||  ||     ||   | |    |  |||| | |||| |||| |||||||| ||||| || ||||||||||| |||||||| ||||| ||||| ||||| || ||||||||||| |||||||||||||| |||
gtgaggttttcctcgaaaatttcacttttcaatcttgcttgctatcatttctcaccgatt---tttttggtaattgtgtttttgcagACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 2
gttcgagatctgttc-ttattctcggtttccgtaattccataaccttcttcttcttt----------ccttgaatctcgtattgttgtttgt-ttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
     |||||| |     ||   |  |  ||  || || ||   |||||||| | ||          | |  ||| ||||  | ||  ||||  ||||||| ||||||||||| ||||| || |||||||| ||||||||||| |||||||| |||||||| ||||| |||||||| ||||||||||| |||
--gtaagatctctcaaccatcaccattaccctcaactcaatcttcttcttctccgttgtgatgtaaccttcaaatttcgt--tattacttgtgctgtagACGTTCAAGCGCAGAAACGGCGGCCGCAACAAGCACGGCCGTGGACATGTCAAGTTCATCCGCTGCTCAAACTGCGGAAAATGCTGCCCAAAG

upper sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S270_77V6.1 (Physcomitrella patens), 3'ss of exon 1
------------gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgttt--gtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
            ||     |  |||      ||| | ||| ||    |   |       ||  | | |  |||   |  |   |||  ||  ||     ||||  ||||| |  | |  |||||||||||||| || |||||||||||||||||    ||| | ||||||||||| ||    |||   ||||||
gattggcgaattgtgttttaattgtctcctatctagattttcgcgggtttgtgtagggtttgatgtgtt-ttggtgcgggggctgtctttcattgtaacagACTGTCAAGAGGCGCAGTGGAGGTCGCAACAAGCATGGCCGTGGCCATGTCAACCCTATCAGGTGCTCCAACTGTGGGCGCTGCGTTCCCAAG

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|6070885|gb|AW100272.1|AW100272
EST:     CTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|192326591|gb|FK018838.1|FK018838
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298198055|gb|HO039594.1|HO039594
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|10238902|gb|BE807798.1|BE807798
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|151411510|gb|EV281321.1|EV281321
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298192759|gb|HO033193.1|HO033193
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|31466786|gb|CD408814.1|CD408814
EST:     CGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298183541|gb|HO028754.1|HO028754
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298182602|gb|HO031337.1|HO031337
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298162975|gb|HO011708.1|HO011708
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|17023090|gb|BM094124.1|BM094124
EST:     GCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: GCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|192296480|gb|FG992316.1|FG992316
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298197741|gb|HO045220.1|HO045220
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCACGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|4405733|gb|AI507882.1|AI507882
EST:     AAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: AAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|298163646|gb|HO012379.1|HO012379
EST:     CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: CACTCAAAAACCTAGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
EST: gi|31474104|gb|CD416132.1|CD416132
EST:     AGAGCGAAGAGCGTGAAGGCACCGGCCGCCGCCCATG                         ACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC
genomic: AGAGCGAAGAGCGTGAAGGCACCGGCCGCCGGCCATGgttcgagatc ... ttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG
    ccataac  putative branch site (score: 3)
                                            tttgttt  putative PPT
                                    tattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgagatctgttcttattctcggtttccgtaattccataaccttcttcttctttccttgaatctcgtattgttgtttgtttgtagACATTCAAGCGCAGGAACGGAGGTCGCAACAAACACGGCCGTGGCCATGTCAAATTCATCCGATGCTCCAACTGCGGCAAATGCTGCCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC