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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA

Basic information

species Glycine max
transcript GLYMA16G29040.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
------------------------------------------actagccatgcagctgaagctgt-atgatt-taaattctaaacttatttccttttactttcccccttttttgtgtt---actatatactaatttcttgcttg-cagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
                                           |||   || ||      |||   | || | ||||      | || ||   | | ||  |  |    | |   |||   ||  | |      ||||| ||   |||||| |||| || |||||||||||||||||||| || ||||||||||| || || | ||||||||| || || ||||  || ||||| ||  ||| ||| |
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctgttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA

upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G159307_T01 (Zea mays), 3'ss of exon 10
--actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttg--tgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
  ||  |  || | | |       |    | |  |  ||| |   |||   ||     ||  |  | | |    ||| | | ||| ||  | |||   | | | |      | || || |||||||| ||||| || |||||||| || || |||||||||||||| || ||| ||||||  ||||||||||| |||||||   
gtacc-gttattctggttgcataattcactgtgtaccctagatgaattaatttaccagttgacaatctgtaaattgtaattttattcttttctct-attagGAAGGGACAGCAGATAATGAGTTTGAAAAGCGTATTAGACCAGAAGTGATACCTGCAAATGAGATTGGAGTTTCATTTGATGATATTGGTGCCTTGGATG---

upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
                     ||| |   | |    |  |||     || | |  | |   |||       ||||  |     |   || |||   |||||||||||| ||||| |||||||| ||||| || ||||||||||| || || |||| ||||||||| || ||||| |  || || || ||  |||  || |
---------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctca---acgttaacagcatttgtgtttttga--gcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA

upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G058491_T01 (Zea mays), 3'ss of exon 10
--------------act-agccatgcagctgaagctgtatgatttaaattctaaacttatt--tccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
              ||| |  | | |||   |   | |   || |     ||| |   | |  |   |  | | ||   || |    |||   | | || |  | |     | | | | |   || || || |||||||| ||||| || |||||||| || || ||||| ||||| || || ||| ||||||  ||||||||||| |||||||   
gtaatgttattctaactgaatctttcagaaaattgttttctatgtgtgccctagaggaactaatttatcaattgtcagtctgtaacttgtacttttttatttttcttccattagGAAGTAACACCCGATAATGAGTTTGAAAAGCGTATTAGACCAGAAGTGATACCTGCTAATGAAATTGGAGTTTCATTTGATGATATTGGTGCCTTGGATG---

upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 3'ss of exon 10
-----actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCC---TGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
       |  || ||||  |   | | |    |||   ||  | |    ||| ||   |   |   ||  | ||   ||||| | |  |||||  ||   | |||   |||||   | |||| || ||||||| ||| ||||| |||||||||||||| |||||| ||||||| ||  ||||||  || |||||||| |||||||   
aaggaggttcccttgcattt---gttttcccctttttgttgaagaaaattttactaagaaaattttccgatattcccttactcttt--taattgtttcgctacagTTGGTTCCACCTTACAATGAATTTGAGAGGCGTATAAGGCCAGAGGTTATCCCAGCAAATCAGATAGGAGTGGCATTTGAGGACATTGGTGCCTTGGATG---

upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 12
actagccatgcagctgaagctgtatgatttaaattcta---aacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCC---TGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
      ||    |||||   |     |   ||||| ||        |||| |  | | |  |   || ||||   |    |  |  |||||  || | | |||||||||||   |||||| || ||||||||||| ||||| |||||||||||||| || ||||||||||| || |||||||  ||||| ||||| |||  ||   
---gatcacaatgctgatttttgtaaaagaaaattttattgggaaaattttccatcattcccttactcttttaactgttgaactgttaattgtttccctccagGAAGTTCCACCTGACAATGAATTTGAGAAGCGTATAAGGCCAGAGGTTATCCCAGCGAATGAGATAGGAGTGACATTTGATGATATCGGTGCTTTGAGTG---

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|31561891|gb|CD487729.1|CD487729
EST:     CCATCCCAATAACGAAGAAAGATGGCGAAAATCCTATACCTGCAAAAGTG                         GAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCC
genomic: CCATCCCAATAACGAAGAAAGATGGCGAAAATCCTATACCTGCAAAAGTGgtaagataaa ... ttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
                                   tactaat  putative branch site (score: 1)
                                         tttcttgctt  CT-rich tract
                           ttactatatactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - -ccatgca
- - - - - - gctgaag
- - - - - - - - - - tgtatga