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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaatcacattcttttctggatggagggagtacatagttacttttccccatgcatcttgtgattcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA

Basic information

species Zea mays
transcript AC209208.3_FGT001
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 5
tagaatcacattcttttctggatggagggagtacatagttacttttccccatgcatcttgtgattcttctaaatgcatctccatata------ttatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
      ||||||||        |  | | | | ||   || |||   | | ||  || | || ||  | ||||   | ||  | |        |||| ||||| ||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||| || ||||| |||||||| || ||||||||||  || ||  |||
-----ccacattctgcag-aattttacgaacttcacttttgcttgcactcctgactcctctgtttactttaaaaataactatacactatccatttattcaaaacagGTTGATGATAAACTTTATATATACCTGGAGTATGTTTCTGGTGGATCCATCCATAAACTACTCCAGGAGTATGGGCAATTTGGTGAACCTGCTATCCGCA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G24970.1 (Glycine max), 3'ss of exon 5
tagaatcacattcttttctggatggagggagtaca----tagttacttttcccca-tgcatcttgtgattcttctaaatgcatct-ccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
       ||||| |||  ||     |   |  | |    |||  |||| |   || |   | |  | | ||| || |  | | || |   ||  |     ||| |||| |  || |||||||||||||| |||||||||||| |||| || || ||| |||| ||||| ||||| |||||||| |||||||||| ||| ||| | |
------tacattttttcttgtcatcactcatcataatattagaaacttgtttacagtatttttcttcagtctacttatagaaactgctgaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 6
tagaatcacattcttttctggatgg-agggagtacatagttacttttccccatgcatctt-gtgattcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
  |  ||   |  |||    |||   |  ||      | || ||   |   ||   | || ||| ||| | || |      ||   ||         || |||||||||| ||||||||||||||||| || ||||| ||||| || || |||||||| ||||| ||||| ||||| || |||||||||| ||  ||| | |
-tgtttctggtggtttatctgataacatagaagtgggaatttctcgacagtatttgtttttgtggttcct-tatagaggcttctgaatcgccccttgaacagGTTGATGACAAGCTTTACATATACCTTGAATATGTATCTGGAGGCTCCATACATAAACTTCTTCAAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 5
tagaatcacattcttttctgg-atggagggagtacatagttacttttccccatgcatcttgtgattcttctaaatgcatct-ccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
  |  | ||||| ||   ||  ||      | || ||| ||  ||| |   ||   |||| | | ||| || |  | | || ||| ||  |     ||| |||| |  || |||||||||||||| |||||||||||| |||| || || ||| |||| ||||| ||||| |||||||| |||||||||| ||| ||| | |
-tggtttacatttttacttgtcatcattatattagatacttg-tttacagtatttgtcttttcagtctactcatagaaactgccaaatcatcccttaaacagGTAGGCGACAAGCTTTACATATATCTGGAGTATGTTGCTGGAGGCTCCATATATAAACTTCTTCAAGAATATGGACAATTTGGTGAACTAGCTATTCGTA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 5
tagaatcacattcttttctggatgg-agggagtacatagttacttttccccatgcatc-ttgtgattcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
  |  ||   |  |||    |||   |  ||      | || ||   |   ||   |  ||||| ||| | || |      || | ||         || |||| ||| | ||||||||||||||||| |||||||| ||||| || || |||||||| ||||| | ||| ||||| || |||||||||| ||  ||| | |
-tgtttctggtggtttatctgataacatagaagtgggaatttctcaacggtatttgttattgtggttcct-tatagaggcttctaaatcaccccttgaacagGTCGATAACAAGCTTTACATATACCTTGAGTATGTATCTGGAGGCTCCATACATAAACTTCTTCGAGAATATGGGCAATTTGGTGAACTAGTTATTCGTA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 4
--------tagaatcacattct-----tttctggatggagggagtacatagttacttttccccatgcatcttgtg-attcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
        || |   |  |  |     ||||||      |  | ||   |  |  ||   | ||  ||  |  || |     ||| || | | | | |        |||   |||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||  |||| ||||| |||||||||||||| ||||||||  | |||||| | |
gtaagttttacagatatttcttggacatttctgttctctgatactat-caactgtttcagctcaaccaagtcatgcacatgactagattc-tttactttcccctcccaattcagGTCGATGACAAGCTGTATATATATCTGGAGTATGTCTCCGGTGGTTCGATCTATAAACTTCTTCAAGAGTATGGACAATTTGGTGAGAATGCCATTCGTA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 3
tagaatcacattcttttctggatggagggagtacatagttacttt-tccccatgcatcttgtgattcttctaaatgcatctccatatattataca-aaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
     |   | | |  |||| ||  |     ||     | |||   |  | ||  ||  |     |  | | ||    ||      |||  | |   || |||| ||||| || || ||||||||   ||| ||||| | |||||| || ||| |||| ||||| ||||||||||| ||||||||||||  ||| |||   |
-tcctttgaagtttcatctgcatt-acattatattagatcactagatggcgattgattcttcagcttatgtgaaattttccttggctatattccttgaacagGTGGATGACAAACTCTACATATATTCGGAATATGTATATGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGTTTGGTGAAATAGCTATTCATA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 6
----tagaatcacattcttttctggatggagggagtaca-tagttacttttccccatgcatcttgtgattcttctaaatgcatctcca-tatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
    | ||| |    |||    |  ||      || ||| ||| |     |     ||  ||||  | || |   ||||    ||    ||||||     ||  |||| ||||| || || ||||||||  |||| ||||| |||||||| || ||| |||| ||||| ||||||||||| ||| ||||||||  ||| ||| | |
tcctttgaagcttcatctgcattacattatattagaacactagatggcgat-----tgattcttcagcttatgtgaaattttccttggctatattccttgaa-cagGTGGATGACAAACTCTACATATATTTGGAATATGTATCTGGTGGTTCCATATATAAACTTCTTCAAGAGTATGGCCAGCTTGGTGAAATAGCTATTCGTA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: PP1S44_113V6.1 (Physcomitrella patens), 3'ss of exon 4
---------tagaatcacattcttttctggatggagggagtacatagttactttt---ccccatgcatcttgtgattct----tctaaatgc----atctccatatattatacaaa-------atagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
          |   | |    | |||    ||  |    |      || || | |   | ||||   ||||||   | |    || | |||     ||||   |   |  |    |         || | || |||| | | || |||||  |||||||||||||||| ||||| || ||||| || ||||||||||||||    ||    || | ||   |  |||
gtgcgacgcaaaccttatgcaccttttaatatttaacatgacgtctgtcacatgttaactccattattcttgttgctttggggtcgacatgtcgggatctgactgcgtcgttgggatcttctggcagTTGGAAGATAGGTTGTATATATATTTGGAGTATGTTTCTGGAGGATCAATCCATAAACTGCTCCAAGAGTATGGCGCTTTCAAAGAGCCAGTGGTGCGCA

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|32837658|gb|CD977336.1|CD977336
EST:     TGAGCCGACTGCAACACCCAAACATTGTGCGATACTATGGATCTGAAACT                         GTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATA
genomic: TGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACTgtatgaactg ... tacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATA
EST: gi|32838212|gb|CD977890.1|CD977890
EST:     TGAGCCGACTGCAACACCCAAACATTGTGCGATACTATGGATCTGAAACT                         GTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATA
genomic: TGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACTgtatgaactg ... tacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATA
EST: gi|91877716|gb|EB407673.1|EB407673
EST:     TGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACT                         GTTGATGATAAGCTTTACATATACCTGGAGTATGTT
genomic: TGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACTgtatgaactg ... tacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 3

GAAATATCACTTCTGAGCCGACTGCAGCACCCAAACATTGTGCGATACTATGGATCTGAAACTgtatgaactg ... tacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccccatgcatcttgtgattcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA
                     ttctaaa  putative branch site (score: 3)
                                     atatattatacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaatcacattcttttctggatggagggagtacatagttacttttccccatgcatcttgtgattcttctaaatgcatctccatatattatacaaaatagGTTGATGATAAGCTTTACATATACCTGGAGTATGTTTCTGGTGGATCTATACATAAGCTTCTCCAAGAGTATGGACAGTTTGGTGAACAAGCCATTTGCA

- - - cacattc
- - - - - - - - -ctggatg
- - - - - - - - - - - - - - - - - - - - - - - - - atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatt