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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGCGGGCGGCGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagtaccgttcgcaatcatccccccctcgcctcgcctcgtcgtctcgccgcgcctcctgcgcccgcgccgctcgtggtttggagtggtagatctg...

Basic information

species Oryza sativa
transcript LOC_Os02g46510.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G331032_T01 (Zea mays), 5'ss of exon 1
GCGAGCGGGCGG-CGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagtaccgttcgcaatcatccccccctcgcctcgcctcgtcgtctcgccgcgcctcctgcgcccgcgccgctcgtggtttggagtggtagatctg-
 || |  ||||| |||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| || ||||| ||||  || || |||   |    | |    | || |     |  |   |    |   ||  |  | |||      | | | |  |      | |    | |  
-CGGGAAGGCGGGCGACGATGCCGGTGGCAGCGTCGGCCATCTACTTCCTCAACCTTCGCGGGGACGTCCTCATCAACCGCCTCTACCGTGATGATGTTGGgtatgttgtgccgcg-gtgggcttggagcgctagatctacggccctgggagggaccgattagttcgcttctagctcgcatcttcgtagatcgcgattatat

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 1
GCGAGCGGGCGG--CGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgta-gtaccgttcgcaatcatccccccctcgcctcgcctcgtcgtctcgccgcgcctcctgcg-cccgcgccgctcgtggtttggagtggtagatctg
  || |    ||  ||  |||||||||||| || || || ||||||||| | || ||||| || |||||||||||||| |||||||| ||||||||||||||||   |   |  |  |  | |||       | | |  |  | |  | |         |     | |     |    | | | |||||||||     | |   
--GATCCACTGGATCGGAGATGCCGGTGGCTGCTTCCGCTATCTACTTCTTGAATCTCCGGGGCGACGTCCTCATCAATCGCCTCTATCGCGACGATGTCGGgtatattcatctctatttctatctctatatctttgtgtgtcttgattggtggaaattggtggtttcaatttgttgagataggggtttggagcacagggta--

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 5'ss of exon 1
GCGAGCGGGCGGCGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagtaccgttcgcaatcatccccccctcgcc-tcgcctcgtcgtctcgccgcgcctcctgcgcccgcgcc-gctcgtggtttggagtggtagatctg
|  || ||  ||  |  |||||||||||||| || |||||||| ||||||||||| ||||| || || |||||||||||  | ||||| || ||||| ||||  |   | | | |     || |  |   ||||   | ||  ||     | |    |  |  |  |   |     |  |   ||  |||||  |  | |  
GACAGAGGTTGGGCAAAATGCCGGTGGCGGCATCTGCCATCTATTTCCTCAACCTTCGAGGAGATGTGCTCATCAACCGGTTGTACCGGGATGATGTGGGgtatgcc-tgctgcttcgcttcgtttctgtctcggagttgctgcgattgttggagatgagttttttgtgtggatttgtgcaacgtgaggagtttttcagcg-

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ22278 (Selaginella moellendorffii), 5'ss of exon 1
GCGAGCGGGCGGCGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagtaccgttcgcaatcatccccccctcgc---ctcgcctcgtcgtctcgccgcgcctcctgcgcccgcgccgctcgtggtttggagtggt---agatctg---------------------------------------------------------------
|   | | ||  |||  |||||||| ||||| || || ||||||||||||||||| |||||||| || |||||||| ||||||||| | |||||||||||||  | | | |         ||  |  |   |||    || |       || ||   | ||  |  | |  |      | || | ||| | || |     |  | |                                                               
GTTTGGGCGCATCGATCATGCCGGTCGCGGCTTCCGCGATCTACTTCCTCAACCTGCGAGGGGATGTGCTCATCAATCGCCTCTACAGAGACGATGTCGGgtaag-aatcctcccaattctctccggcatttcgagcgctagatctagggtgtcctggggcagcacggggtcatatttcgcgagcttttgggtcggctggggcccgagatccagctccggagtgagaatttagggctcttagagtgactggctacgtttaattttgcag

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ25669 (Selaginella moellendorffii), 5'ss of exon 1
GCGAGCGGGCGGCGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagtaccgttcgcaatcatccccccctcgc---ctcgcctcgtcgtctcgccgcgcctcctgcgcccgcgccgctcgtggtttggagtgg---tagatctg---------------------------------------------------------------
|   | | ||  |||  |||||||| ||||| || || ||||||||||||||||| |||||||| || |||||||| ||||||||| | |||||||||||||  | | | |         ||  |  |   |||    || |       || ||   | ||  |  | |  |      | || | ||| | || |     |  | |                                                               
GTTTGGGCGCATCGATCATGCCGGTCGCGGCTTCCGCGATCTACTTCCTCAACCTGCGAGGGGATGTGCTCATCAATCGCCTCTACAGGGACGATGTCGGgtaag-aatcctcccaattctctccggcatttcgagcgctagatctagggtgtcctggggcagcacggggtcatatttcgcgagcttttgggtcggctcgggcccgagatccagctccggagtgagaatttagggctcttagagtgactggctacgtttaattttgcag

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|88591176|gb|CI708095.1|CI708095
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCA
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCA
EST: gi|88731589|gb|CI755202.1|CI755202
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATG
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATG
EST: gi|88728360|gb|CI751870.1|CI751870
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|87006800|gb|CI285834.1|CI285834
EST:     GACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: GACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|88352377|gb|CI615631.1|CI615631
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|95100746|gb|CI692457.1|CI692457
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|14192041|gb|AU184252.1|AU184252
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|58653067|gb|CK041747.1|CK041747
EST:     AACCTCCGAGGGGACGTCCTCATCAAGCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|88339495|gb|CI635473.1|CI635473
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|88448565|gb|CI693954.1|CI693954
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|7219924|gb|AU063368.2|AU063368
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTC-G                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|88721770|gb|CI745069.1|CI745069
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|88424575|gb|CI606374.1|CI606374
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
EST: gi|58693506|gb|CK082193.1|CK082193
EST:     AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGG                         GGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT
genomic: AACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACT

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: 54 (upstream exon), 74 (downstream exon)
Score: 10

GCGAGCGGGCGGCGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagta ... gactatacagGGGAAATATGGTTGATGCATTCAGGATGCACATTATGCAAACAAAAGAACTGGGTACATGCCCTGTTCGGCAAATAGGAGGCTGTTCATTCCTTTACATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGCGGGCGGCGACGATGCCGGTGGCGGCGTCGGCCATCTACTTCCTCAACCTCCGAGGGGACGTCCTCATCAACCGCCTCTACCGCGACGATGTCGGgtgcgtagtaccgttcgcaatcatccccccctcgcctcgcctcgtcgtctcgccgcgcctcctgcgcccgcgccgctcgtggtttggagtggtagatctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagtgg