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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG

Basic information

species Glycine max
transcript GLYMA10G04410.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 5
-------------------------------ttatagtattttgggtatctatatga-atggtgtttaagatagt--gttcttcgacatcttttttttgagtgcttgtaatttttgaatgt---gtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                               |   |   | ||  | ||  |  ||  ||    | |   ||  |   ||  || |    ||     |    | ||  |  |||||| ||     |||  ||| ||||| || ||||| || |||||||| || || |||||||||||||||||| | || || |||||||| ||||| ||||||||
gttagtagctagcaaatgtgccaacaatcattagaaacttcttcagaattcacctgttattccttgtgtcattatctatttctcaatgcattcagaattttcgtttccatgttttgactggcagttaatgatttcagGCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttt-tgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                 ||  ||   ||  | ||||  |     |   ||||  ||||  | |   | |  || | |    |||   |     |   ||||||||| || || || || |||||||| || || ||||||||||||||| |||||||||| || |||||||||||||| ||
----------------gtcagtaatcatttt-tttaccacttgatgactcgatctcttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
--ttata-gtattttgggtatctatatgaatggtg---tttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
  | ||  || |       || || |  || |  |   |||    |     |    |    |||| ||||   |   |||||| ||   || |   ||| |||||||||||||| || ||||| |||||||| ||||| |||||||||||| | ||||||||||||||||||||||||||||||||
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttt---tttctgtaatgttc--atattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------ttatagtattt-----tgggtatctatatgaatgg---tgtttaagata-gtgttcttcgacatcttttttttgagtgcttgt-aatttttgaatgtg-----taaacattgc-----agGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                                                                             ||  ||||  |      | | ||  |   |  |       ||| |||||  ||  ||  |   | | ||||| ||   || || ||   |  | | |       |    ||||     |||| ||||| ||||| || || ||||| || || ||||| ||||| || |||||||| |||||||||||||| ||||| ||
gtatgtttacctcttctttttctgcgcattcttctttcctccaaactactccttgatcgtatggttaataaatggtattccagtacctgcgcgcgagaattcacgcgcgtacattctttttagatatatgacctgtggtttttatttttcgaccactagtcaaacatcaagtattaattccaggttttgctcatcagGCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                                                                     | |  | || | ||| |  |||   | || ||  |||    ||    || |    |  | | | |   |  ||| |     || || |   |||| ||||| ||||| ||||| || || ||||||||||||||||| ||||| ||  |||||||||| ||||||||||| ||||| ||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacaga-ggagtgcaag----tggcactccattgatcatctgtaatctcaagtattgacacaaagtttcg-catt-cagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------ttatagtattttgggt---atctatatgaat--------ggtgtttaagatagtgttcttcgacatcttttt--tttgagtgcttgtaatttttgaatgtgtaaacattg------cagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                                                           ||  ||  |   || |   |  | |||  ||        | |||   |  |   | ||   ||  |  |  |  | |  | || | || ||||    | |  | |||  |      ||||| ||||| ||||| || || ||||| ||||| ||||| ||||| || |||||||| |||||||||||||| ||||| ||
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattg-cagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                                         |||     |     |||  |||||     |    ||||||   |  ||   | ||  ||||||||||| || || || || ||||||||||||||||| ||||||||  ||||||| || || |||||||| ||||||||
-----------------------------------------gtgcgtagcttgtacttccttttg-----tcccgatttttatctaagtgttctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

upper sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattg-cagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                                         |||     |     |||  |||||     |    ||||||   |  ||   | ||  ||||||||||| || || || || ||||||||||||||||| ||||||||  ||||||| || || |||||||| ||||||||
-----------------------------------------gtgcgtagcttgtacttccttttg-----tcccgatttttatctaagtttcctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

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|9986562|gb|BE660670.1|BE660670
EST:     GCTCACAACAGGAACAACTGCAACACTGGCAAATAAACAGGAGAACACTT                         GCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTG
genomic: GCTCACAACAGGAACAACTGCAACACTGGCAAATAAACAGGAGAACACTTgtaagttccc ... aacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
                         ttgtaatttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatagtattttgggtatctatatgaatggtgtttaagatagtgttcttcgacatcttttttttgagtgcttgtaatttttgaatgtgtaaacattgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA