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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgtacag

Basic information

species Oryza sativa
transcript LOC_Os05g40820.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g40820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G142640_T03 (Zea mays), 5'ss of exon 2
GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgtacag
||| || |||||||| || || ||||||||||| ||||| ||||| |||||| | ||||| ||||||||||| ||||| |  ||     |   ||  ||  |   |  |    |   || |       |   ||| | | ||     |   | | || || ||
GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAGgtta--ctcgctgttacattttta-taagagatttataagcttatagaaaatgtttgttatggaaagaacttacatttgttctatag

upper sequence: LOC_Os05g40820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G074898_T01 (Zea mays), 5'ss of exon 3
GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgt-acag
||| || || ||||| || |||||||||||||| ||||| ||||| ||||| || ||||||||||||||||| ||||| |   || |  |  | |  |||   ||   |    |  ||| | |    |  |  || | | ||    ||   | | || |   ||
GACGGAACTCTGCCGCTTCAGTGGCCAGAAGATCTATCCTGGGAAAGGCATCCGGTTTATTCGTGCTGATTCTCAGgttac-ttgctgttacattttttgtaataggtttgtaagctttatatagc-atgatcttatggcaaggaaatacatctgtttttgtag

upper sequence: LOC_Os05g40820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G110328_T04 (Zea mays), 5'ss of exon 3
GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgt----tgtaaacgtattg-gtatattgtacag
|||||| || ||||| || || ||||||||||| ||||| ||||| ||||| || ||||| ||||||||||| ||||| |  ||    |||  ||  |||          | || || |||  | ||| ||  |  |    || |||   | |   ||| || || ||
GACAGAACTCTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATCCGATTTATCCGTGCTGATTCTCAGgtta--ctagctatcatatttttgt---------aagagatgtctaagattataaaatcttcttatggaaagaaactacatatgttttatag

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|396941383|gb|HO188592.1|HO188592
EST:     AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|33810488|gb|CF331132.1|CF331132
EST:     AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCCCAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|89167279|gb|CI252810.1|CI252810
EST:     AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|8324524|gb|AU091671.1|AU091671
EST:     AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|5607423|gb|AU076121.1|AU076121
EST:     AGAAGATATATCCA-GGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: AGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
EST: gi|88397656|gb|CI684589.1|CI684589
EST:     GAAGATATATCCAGGGAAAGGGCATTCGCTTTATTCGTGCTGATTCACAG                         GTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG
genomic: GAAGATATATCCAGGG-AAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTG

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: 75 (upstream exon), 73 (downstream exon)
Score: 342

GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgt ... tattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAGAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAGgtcaggctgttcatcgaatgattgctttaatgtcaggatatttctctgcttagaaggttgttgtaaacgtattggtatattgtacag

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