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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactacttgacttcttcaatctagctagcctaggaatcttgtttacctactagtaccagtaataaaaacaactctttctatattctttccacatagtactaatttctccctcatgtctcaacag

Basic information

species Oryza sativa
transcript LOC_Os03g01150.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01150.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G374779_T04 (Zea mays), 5'ss of exon 3
TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccac-----tacttgacttcttcaatctagctagcctaggaatct--tgtttacctactagtaccagtaataaaaacaactctttctatattctttccacatagtactaatttctccctcatgtctcaacag
 || || || || |||||||||||||||||| | |||||||||||  ||||||||  |     | ||  ||   |||  |  | |     ||  |||    |||| |     | ||  |||||| | |    |   | ||   |                                          
AGAGATTGGCAGAGGAACATGGGACTCTTGGGTCATGCCTCTTCAACAACAGgtcttcatcgatcctctacacattcttttcatccttgttataaattaaatgttcataggttggt-tcagtaacacatttgatcatgtccgcag-----------------------------------------
















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|88577066|gb|CI673617.1|CI673617
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88432450|gb|CI567489.1|CI567489
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|29619262|gb|CB624274.1|CB624274
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88340848|gb|CI637008.1|CI637008
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|66916126|gb|CX102974.1|CX102974
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|29661631|gb|CB657906.1|CB657906
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|11025710|gb|AU162311.1|AU162311
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88324289|gb|CI566102.1|CI566102
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88735407|gb|CI758915.1|CI758915
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88447741|gb|CI579817.1|CI579817
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|58678057|gb|CK066744.1|CK066744
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88389314|gb|CI598112.1|CI598112
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|25797306|gb|CA753267.1|CA753267
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|117235882|gb|CT847837.1|CT847837
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG
EST: gi|88743128|gb|CI766636.1|CI766636
EST:     AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAG                         GCTGATATTGTTTGCAGTAAG
genomic: AAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG

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: 52 (upstream exon), 21 (downstream exon)
Score: 26

TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactact ... gtctcaacagGCTGATATTGTTTGCAGTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAATCGGAAGTGGAACATGGGACTCTTGGTTAATGCCTCTTCAGAAACAGgtccactacttgacttcttcaatctagctagcctaggaatcttgtttacctactagtaccagtaataaaaacaactctttctatattctttccacatagtactaatttctccctcatgtctcaacag

- - - - - AGTGGA