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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaagcttcatgcgtttcgttccttattttcattcatttgttgctcaaaatcgttgttccctttgttatcagtcactccatcacatagaaaggg...

Basic information

species Oryza sativa
transcript LOC_Os01g39380.2
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GRMZM2G074466_T01 (Zea mays), 5'ss of exon 4
TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaagcttcatgc-gtttcgttccttattttcattcatttgttgc----------tcaaaatcgttgttccctttgttatcagtcactccatcacatagaaaggg
|||||||||||||||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||  |||     |||| |||    |   | || |   | | || || |            |  |||   | || ||||||||| || ||  ||| ||           
TATTACTGCTCTTCATTGCGTAACAAGAAAGGAGGTCTGGGATCTTGTTGGTGATCGTGAAGATGCTGGTTTTTTCATCAGCGGAAGCACAGATTGCACGgttagcttaaatcatatgctgttatacttactcttgttggttactttttacaatacttgctctagcatcacagctcactttgttattaggcatgccagca-----------

upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GLYMA08G04510.1 (Glycine max), 5'ss of exon 23
TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaagcttcatgcgtttcgttccttattttcattcatttgttgctcaaaatcgttgttccctttgttatcagtcactccat-cacatagaaaggg----
 ||||||||||| |||||||| ||||  | ||| || |||||| | |||||||| |||||||||||||| ||||| || ||||||||||| || ||| | || ||  | |   ||   |   | |        |   | | | ||||| |      |  | || |||    | |   |  |  |  | ||  |  |||       
CATTACTGCTCTCCATTGTGTTACAAAAAGAGAAGTGTGGGATTTGGTTGGTGACCGTGAAGATGCTGGTTTTTTTATTAGTGGAAGCACCGACTGCTCAgtaagtttcaatatctatcacatggaataac-ctggtactgagttgtttcattgccttctggtacccagaatgaggtgatatgctgttcatgtgcaaatatgcag

upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GLYMA05G35210.1 (Glycine max), 5'ss of exon 6
TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaagcttcatgcgtttcgttccttattttcattcatttgttgctcaaaatcgttgttccctttgttatcagtcactccat-cacatagaaaggg----
 ||||||||||| |||||||| ||||  | ||| || |||||| | || |||||||||||||||||||| || || || |||||||||||||| ||| | || ||  | |   ||   | | | |        |   | | | ||||| |      |  | || |||    | |   |  |  |  | ||  |  |||       
CATTACTGCTCTCCATTGTGTTACAAAAAGAGAAGTGTGGGATTTGGTCGGTGATCGTGAAGATGCTGGTTTCTTTATTAGTGGAAGCACAGACTGCTCAgtaagtttcaatatctatcatatggaattac-ctggtactgagttgtttcattgccttctggtacccagaatgaggtgatatgctgttcatgtgcaaatatgcag

upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 24
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 5'ss of exon 23
TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaagcttcatgcgtttcgttccttattttcattcattt-gttgctcaaaatcgttgttccctttgttatcagtcactccatca--catagaaaggg-
| |||||||  | |||||||||||||| | |||||| ||||||||||| ||||||||||||||||| || || || ||||||||||||||||| |||  ||| |   |  |    ||  | || |||  ||      |   ||||   |||   |||   |        |||||   |||    |  | |    | |  || | 
TGTTACTGCATTACATTGTGTAACAAGAAGAGAGGTGTGGGATCTTGTGGGTGATCGTGAAGATGCAGGTTTCTTTATCAGTGGAAGCACAGACTGCTTGgtaaaattgtgt---atttgattggttatttgcaccaaaaaatttcaatgcatgaaaat-taaacatggttgttggtagtttgactgtgagttgtggttagtgg

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|29641894|gb|CB646901.1|CB646901
EST:     GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACG                         GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
genomic: GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
EST: gi|33690825|gb|CF319064.1|CF319064
EST:     GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACG                         GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
genomic: GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
EST: gi|58694147|gb|CK082834.1|CK082834
EST:     GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACG                         GTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT
genomic: GTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTT

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: 73 (upstream exon), 55 (downstream exon)
Score: 28

TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaa ... cattttacagGTAAAAATATGGGATCCAAGTTTGCGTGGTTCTGAACTTCGGACAACACTTAAAGGGCACACTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTACTGCTCTTCATTGTGTAACAAGGAAAGAGGTTTGGGATCTTGTTGGTGATCGTGAAGATGCTGGCTTTTTCATCAGTGGAAGCACAGATTGCACGgttaggctaagcttcatgcgtttcgttccttattttcattcatttgttgctcaaaatcgttgttccctttgttatcagtcactccatcacatagaaaggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG