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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttccactgttttcagttgcattgcttgttttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag...

Basic information

species Oryza sativa
transcript LOC_Os01g17020.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G078895_T02 (Zea mays), 5'ss of exon 2
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttccactgtttt-cagttgcattgcttgttttctaccgaacaat--aaattgctatacttttttttatagccgcaacacattatgaaagag
|||||||||||||||| |||||||||||||||||||| ||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||||||| ||||    ||||  || ||||    |    ||  ||||  | | ||    | | ||||  |||||||  ||     |  | |  | |  |     | ||  |   
TACCTGCATTATCACCTTGTGCAACAACTCTTCCAGTTTTTCTTGCTGTTGGCAACTCTTCCTCAATGATGATTCTTGCAATCATTGTGCTCCTCTTCAGgtcttcaccctctttcactccactgtttttttattgtatttgttggtactaccaattcaaattgcattatcacgtccttt--ctgttattgggtttgttaac-

upper sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G44180.1 (Glycine max), 5'ss of exon 2
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttcc---actgttttcagttgcattgcttgtt-ttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag
| |||||||| || || ||||| ||||| || ||||| |||||||||||||| ||||| || ||||||||| | ||||| ||||| || || || || ||||   || |  |||||   |    | | | ||      | || | || |          |||     |||||||| ||      |      |||  |       
TCCCTGCATTGTCTCCTTGTGCTACAACACTCCCAGTATTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtatttatcaatttccttaagcaatatgattttttcctcctgctattttgttctttttcaaacgtgcatacttttcttctgcttccatgtgcatgtttgg----

upper sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G04600.1 (Glycine max), 5'ss of exon 2
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttccactgttttcagttgcattgct-tgttttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag-
| |||||||| || || ||||| ||||| || || || |||||||||||||| ||||| || ||||||||| | ||||| ||||| || || || || ||||    | |  |  ||  | |  | | ||  | || | |||| | |   |   ||    |  |  |  || |   ||         |  ||  |||      
TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcc--tatgattatttaaagtgatatgttatttgttggtaaaacggtgtcagtgattatcaataataaaaattctgatgttgaccttaa

upper sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 2
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttc-cactgttttcagttgcattgcttgttttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag
| || || || || || |||||||| || ||||||||||||||||| ||||| ||||| |||||||||||| | ||||| || || ||||| || || ||||    |   | |    | ||   ||    |||||  |  ||   |     ||  |   |    | |||| || |   |  |  |  |||        | |
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgcatttttctttccttgattcact-tgtttcttgacacttcttctagcaaacatagaacagagcatctgtg

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|86822669|gb|CI251769.1|CI251769
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|58604169|gb|CK014697.1|CK014697
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|88483538|gb|CI420809.1|CI420809
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTGTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|218490492|gb|FG962756.1|FG962756
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|88966154|gb|CI013030.1|CI013030
EST:     TGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: TGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|33819861|gb|CF335747.1|CF335747
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|86823111|gb|CI254015.1|CI254015
EST:     GGCAATACATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|88485707|gb|CI422978.1|CI422978
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|86833762|gb|CI337336.1|CI337336
EST:     -GCAATTCATCCTCCATGATGATCCTGGCGATCATTGTGCTCCTCTTTAG                         TACCATCACAATGATGACATCCTTGTTGGCCCTCTCATTCTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG
EST: gi|88473034|gb|CI410305.1|CI410305
EST:     GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAG                         TACCATCACANTGATGACATCCTTGGTGGCCCTCTCATTTTACGGTGCTAG
genomic: GGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAG

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: 65 (upstream exon), 73 (downstream exon)
Score: 16

TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtaccc ... ccacttgcagTACCATCACAGTGATGACATCCTTGGTGGCCCTCTCATTCTACGGTGCTAGCCAGATTAAGTTCCACTGGGTGGAACGTTACGACAAGATCCTTGTCGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttccactgttttcagttgcattgcttgttttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctttc