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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG

Basic information

species Glycine max
transcript GLYMA05G32850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
gattaagaacagggatta-ataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaattt--ttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTG-TTGCGGTGGTGGA--TCAGAAAGTGGCCAAGTTATCAG
  ||||      |||||  || || | |  |   ||| | |    ||||| |||||   ||     |||||  ||| |  | | ||| ||  ||  || |||||| |||||||||||  |||||||||| ||||||||||||||     | ||||||   |  || |   |||| || | |  |  |||  ||    ||  |    
--ttaattgggcggatttcatcatatatttattgttg-tgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGAT-GAGCCACG--

upper sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 2
gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataatatgtgatttg--gacaatttttttaactgttgtgctta--ttggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG
    || |||     |||  |      |     |   ||    |  |||  |      ||||   | |||||   |   | || || |||  ||    | |||| | ||||||||||| ||||||||||| ||||||||||| ||   ||| |||| |||| |    || |  |  |  ||  |      | |   |    | |
--ccaaaaacttt--ttaccaccaccactcgcatgcattccacatcaatcttgatcactttgctaataatttcagttttttttttggttaatttttttttgcagTTGGATGATTGGGTGTTGTGCCGAATCTACAACAAGAAGGGAGTGATCGAGAGGTACGACACGGTGGACGCCGGCGAGGACGTGAAGCCGGCGGCGGCGG

upper sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 2
-gattaagaacagggatta--ataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTG-CGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG
  ||     |   |   ||   |  ||||  |  | | | || ||| | |       ||||||  ||   ||||  |  | ||| |  || |||   | |||| | |||||||||||  |||||||||| ||||||||||||||   | | ||||||   |  || |  | |||  | |     |  ||  |||| |       
aaatcgtataattgttctacctttttgttggatggatagatttggtggtatgggc--gtgattaagatttttttcctctcggtttttttt-ttgctgttgcagTTGGATGATTGGGTGCTGTGCCGAATCTACAACAAGAAAGGCGCGCTGGAGAAGCCGACCGGAGCCGGCGGCAGGGCCGAGGCCAGCAGCCAGGGCGCGC-

upper sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG---
   ||||  | |    | || |  ||    |   |  ||  ||   ||| ||    ||||| ||  |||   ||   ||| |||  | |||   |  |||||||||||||||||||| || ||||| |||||||||||||| |  || ||||||||   |      ||||  | | | | ||      | |   |  | |   
--gtaagttctgtttcttattaacttatgtatcatcttttcgtg--aatgat----gatttagattattaactttgttgtggtgggttttgctgta-cagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTA---TTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC

upper sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 2
gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataat-atgtgatttggacaatttttttaactgttgtgcttattggaatg--gcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCC-AAGTTATCAG-----
  | |        ||||  |||| ||      |||  || | |     | || |||     | ||  ||  ||       || |  |  ||| |||   |||||||||||||||||||||||| || || ||||| |||||||| |  || ||||||||      | |  ||| || || | |||||  | |  ||   || ||     
-gtaagcttttctgatttttaat-ttctgggttttttttcgatttttgtgatgatgatgaattgatgatgattaatgggttttttttggttgaaattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAGAAGTA------TTTACCGGCGGCGGCTGAGAAACCGACGGAAAAGATGAGTACGT

upper sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 2
----------gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG-
           |||    ||    |||||  || |||     ||   | |   | ||| || | | |   |||    |||| || |    | |  ||||||   | ||||||||| |||||||| || || ||||| |||||||||||||| |     |||||  |  |     |||        |   |  || |  |||     | |  
gtacgattgtaattctatactac-attaaagatatttatttattatttaaaaaaaaaagaaaaagagtgatggttctttttattgatatatattattattgactttgcagCTTGACGATTGGGTCTTATGTCGAATATACAACAAGAAAGGCAGCGCCGAGAAACAGCACACCTTTG-ATCAAAAGTCAATGAAATATCCAGAACTTGAAG

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|26269515|gb|CA820578.1|CA820578
EST:     ACGTCGACAGATCCGCCTCNNNNNNNNNCACCACCACCAACAACTTGAGG                         CTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
genomic: ACGTCGACAGATCCGCCTCAAAAAAAAACACCACCACCAACAACTTGAGGgtatgtcccg ... ggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
EST: gi|254349194|gb|GR859939.1|GR859939
EST:     ACGTCGACAGATCCGCCTCNNNNNNNNNCACCACCACCAACAACTTGAGG                         CTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
genomic: ACGTCGACAGATCCGCCTCAAAAAAAAACACCACCACCAACAACTTGAGGgtatgtcccg ... ggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
EST: gi|16996945|gb|BM086317.1|BM086317
EST:     ACGTCGACAGATCCGCCTCNNNNNNNNNCACCACCACCAACAACTTGAGG                         CTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
genomic: ACGTCGACAGATCCGCCTCAAAAAAAAACACCACCACCAACAACTTGAGGgtatgtcccg ... ggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
EST: gi|254345780|gb|GR859427.1|GR859427
EST:     ACGTCGACAGATCCGCCTCNNNNNNNNNCACCACCACCAACAACTTGAGG                         CTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
genomic: ACGTCGACAGATCCGCCTCAAAAAAAAACACCACCACCAACAACTTGAGGgtatgtcccg ... ggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
EST: gi|16346015|gb|BI971610.1|BI971610
EST:     ACGTCGACAGATCCGCCTCNNNNNNNNNCACCACCACCAACAACTTGAGG                         CTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG
genomic: ACGTCGACAGATCCGCCTCAAAAAAAAACACCACCACCAACAACTTGAGGgtatgtcccg ... ggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG
                         ttttaac  putative branch site (score: 2)
                    aatttttttaactgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - -agaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttat