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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaaacctactataattagggtatgcatgtatgattgtgtagacattcataatttcacattg...

Basic information

species Oryza sativa
transcript LOC_Os02g48964.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G109039_T04 (Zea mays), 5'ss of exon 2
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaaacctactataattagggtat---gcatgtatgattgtgtagacattcataatttcacattg
 ||||||||||||||||| ||||| ||||||||||| ||| ||||||| |||||||| || ||||| | |||||||||||||||||||||||||||||||||| || | ||| |||| || |  |   ||    ||   | ||  | ||||| || |    |   |   ||   ||| |    |  | |||  ||  |||   
CGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttctttggtttcttagctatttctg---ttaccttaatgttctatatttggatcttcttgttggtgctattattacaaggtacatctttctacacat

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G048045_T01 (Zea mays), 5'ss of exon 8
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacacc--ttgcttttggtaaacctactataattagggtatgcatg-tatgattgtgtagacattcataatttcacattg
|||||||||||| ||||| ||||| || |||||||| ||| ||||||| |||||||| || ||||| | ||||||||| |||||||||||||||||||||||| ||   ||| | || || |  |   |  || | |||        || |   ||     | |   || ||| |||    ||  |    |   | |||||  
TGTTCACTTCATCGCATCAAATAACGATTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTGCAGTTTGAATGGCCAGTGAATgtaggttcctttggcttcttagctatttccgttacctttatgttctatatttggatcttcttgttggtgctatcattaca-aggtacatctttctacacat--

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaa-acctactataattagggtatgcatgtatgattgtgtagacattcata-atttcacattg--
|||||| |||||||| || || ||||||||||| || ||||||| |||||||||||| |||||||| |  ||||||||    |||   |||||||| |||||||||  ||    |||  || |    || || |||   ||| |  ||  | | ||    |||   ||| |   || ||| | ||  ||| || |  | ||   
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgatttt----ccatgttttaaataatagatatgacatttttattattattgttttgatgggtatatatatatatatattgctttatc

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G12970.1 (Glycine max), 5'ss of exon 5
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaa-acctactataattagggtatgcatgtatgattgtgtagacattcataatttcacattg---
|||||| |||||||| || || ||||||||||| || ||||| | |||||||||||| |||||||| |  ||||||||    |||   ||||||   |||||||||  ||    |||  || |    || || |||   ||| |  ||  | | ||    |||   ||| |   || ||| | ||  |||  |  | ||     
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAATgtaagtacttccactttgatttt----ccatgttttaaataatagatatgacatttttattattattgttttgatgggtatatatatatatatatatatatata

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA09G02070.1 (Glycine max), 5'ss of exon 8
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaaacctactataattagggtatgcatgtatgattgtgt-agacattcataatttc-acattg
|||||| |||||||| || || ||||||||||| || ||||||| |||||| ||||| |||||||| |  ||||||||    |||   |||||||| ||||||||| ||||   || ||||   |    ||   ||   ||   |   |  | |  ||||||   || || ||||  | | |       |||||  |||   
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATTGAGAGATTTCAGCTTTCAAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtattttcacttgattttccatgttttaaattaattatgacattttcattatgggtatatgtg-attattgcatcataggcctggaattttgacaaa-

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|86886604|gb|CI322836.1|CI322836
EST:     TGGAGA-GTTTCAGCTCTACAACCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGNGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|218482014|gb|FG963446.1|FG963446
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|29677180|gb|CB673455.1|CB673455
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|29671103|gb|CB667378.1|CB667378
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|163922839|gb|EG712235.1|EG712235
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|218488856|gb|FG965224.1|FG965224
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|25801428|gb|CA757389.1|CA757389
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|58685293|gb|CK073980.1|CK073980
EST:     GGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: GGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|86868119|gb|CI331871.1|CI331871
EST:     GGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: GGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|218501212|gb|FG955432.1|FG955432
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|86479527|gb|CI122160.1|CI122160
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|27548190|gb|CA766256.2|CA766256
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|29619649|gb|CB624661.1|CB624661
EST:     AGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: AGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|29619648|gb|CB624660.1|CB624660
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|29672639|gb|CB668914.1|CB668914
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|2797334|gb|AA750628.1|AA750628
EST:     GGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: GGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|218495836|gb|FG960244.1|FG960244
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|29679291|gb|CB675566.1|CB675566
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
EST: gi|86862373|gb|CI345493.1|CI345493
EST:     TGGAGA-GTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCAGTTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGA
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCA-TTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGA
EST: gi|29674117|gb|CB670392.1|CB670392
EST:     TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT
genomic: TGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGAT

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: 74 (upstream exon), 73 (downstream exon)
Score: 59

TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttt ... ggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaaacctactataattagggtatgcatgtatgattgtgtagacattcataatttcacattg

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC