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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattggttcttcactgttagttttgttgacttgtttatgctactactttgtctaacattgcacatgttgtttttgcaattccattgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG

Basic information

species Oryza sativa
transcript LOC_Os02g29320.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g29320.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G149115_T01 (Zea mays), 3'ss of exon 1
ccattggttcttcactgtta--gttttgttgacttgtttatgctactactttgtctaacattgcacatgttgtttttgcaattccattgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG
| |   ||   |   | |||  ||| || ||   | |  |      ||| ||    |  ||| ||             |      |     || |||  ||||||||||||||||||||| ||||||| ||||| |||||||| || ||||||||| ||||||||||||| || ||||| || || || || || |  ||||
caagctgtgtgtgtgttttaatgttctgctgcgctatc-agatgtttacatttgtgactattccatggtccccgccgactgacgaaacacgtggcaag-cagATGATGGGGCAAGTGAACAGGGAGAGGCTGGCGGAGTTTCTCGGCGAGCTGCAACGGAAAGAGGACACGAACGACAGGTACGTGGCCGCGCTGAGGGGGG

upper sequence: LOC_Os02g29320.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G02900.1 (Glycine max), 3'ss of exon 1
ccattggttcttcactgttagttttgt--tgacttgtttatgctactactttgtctaacattgcacatgttgtttttgcaattccattgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG
  | | |   || || |  |  |||    |   || |||  | |  |  | | |||     || |  |  |  |  |  | || | ||  || |   | ||||||||||||||||| ||    ||||||||||||||||  || |||||||| ||  | |||||||| || |||||| | ||||||||||| || | ||| |
taagttgaatttaacagccaagtttacacttgtttctttgaggtgattttctttctt-tggtgaaagtcctaataatctagttgcttta-attatgtatcagATGATGGGGCAAGTCAATAAAGAGAGACTGGCAGAGTACCTGGGAGAGCTACAGCGTAAAGAGGATACGAATGACCGCTATGTTGCTGCTCTAAGAGGAG

upper sequence: LOC_Os02g29320.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0085g00990.t01 (Vitis vinifera), 3'ss of exon 1
ccattggttcttcactgttagttttgtt--gacttgtttatgctactactttg--tctaacattgcacatgttgtttttgcaattcca-ttgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG
        | |  ||| | |  |  |||  || ||  | ||| | ||  |     | |    |  ||||     ||||  || ||    ||| ||   |   |||||||||||| |||| || |  ||||| |||||||| |||||||| || |||||  | |||||||| ||||||||| | ||||||||||| ||   ||| |
-----aactgtctactatgaaatgggtttcgattttgtgatggttctcttgaagttttgttttcccacaaacatttttgacagttttgcttgaatcgaatggcagATGATGGGGAAAGTAAATCAAGAGAGGCTGGCAGAATTTCTTGGGGAACTGCAGCGTAAAGAGGATACAAATGACCGGTATGTTGCTGCTCTGCGAGGAG

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|44677759|gb|CR291193.1|CR291193
EST:     CCCAGTCTCGAGGCCCACGTCCGGCTCCACCGCCGCGCCCCGAGACCGCG                         ATGATGGGCCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
genomic: ACCAG-CTCGAGGCCCACCTCC-GCTCCACCGCC-CGCCCCGAGACCGCGgtgcgcgccc ... gacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
EST: gi|88419021|gb|CI508974.1|CI508974
EST:     CCTCCGCTCCACCGCCCGCCCCGAGACCGCG                         ATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
genomic: CCTCCGCTCCACCGCCCGCCCCGAGACCGCGgtgcgcgccc ... gacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
EST: gi|56158564|gb|AU096496.2|AU096496
EST:     ACGACCAGCTCGAGGCCCACCTNCGCTCCACCGCCCGCCCCGAGACCGCG                         ATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
genomic: ACGACCAGCTCGAGGCCCACCTCCGCTCCACCGCCCGCCCCGAGACCGCGgtgcgcgccc ... gacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
EST: gi|58692512|gb|CK081199.1|CK081199
EST:     CCCACCTCCGCTCCACCGCCCGCCCCGAGACCGCG                         ATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG
genomic: CCCACCTCCGCTCCACCGCCCGCCCCGAGACCGCGgtgcgcgccc ... gacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTG

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: 71 (upstream exon), 72 (downstream exon)
Score: 9

TGTCCCGGGCGTCGTCGGCTACGGCGTGATGCAGCTCACCAGCTCCCGCAACGACCAGCTCGAGGCCCACCTCCGCTCCACCGCCCGCCCCGAGACCGCGgtgcgcgccc ... gacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttgtctaacattgcacatgttgtttttgcaattccattgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG
     gtctaac  putative branch site (score: 9)
                      ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattggttcttcactgttagttttgttgacttgtttatgctactactttgtctaacattgcacatgttgtttttgcaattccattgtatgacaaaacagATGATGGGGCAAGTGAACCGGGAGAGACTGGCAGAGTTTCTTGGAGAGCTGCAAAGGAAAGAGGACACAAATGACAGATATGTTGCTGCCCTCAAAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - ttcactg
- - - - - - - - - - - -ttgttga
- - - - - - - - - - - - - - - - - - - tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca