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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttatcaattaactattgctgtatttaattccttgaacttcattaggaaaagagtagcatgtgtgtattgagactcacttttgatttcttcatctgtctattctgcttcccttctcattgtgaattgtacctatcctaacatgttctattcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.4
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
gtatttttatcaattaactattgctgtatttaattccttgaacttcattaggaaaagagtagcatgtgtgtattgagactcacttttgatttcttcatctgtctattctgcttcccttctcattgtgaat--tgtacctatcctaacatgttct-attcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG
                                                                  | ||  || | | ||| ||||   || |||      || | | ||    | |||   | |  ||  ||||| | |  ||| || |  | ||| |  ||||||||||||| || || || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||||||||| |||
----------------------------------------------------------------actatgggtt-atagtcattttt--cttattctctatactgtaccgccatgcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG

upper sequence: LOC_Os04g59494.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G312026_T01 (Zea mays), 3'ss of exon 13
gtatttttatcaattaactattgctgtatttaattccttgaacttcattaggaaaagagtagcatgtgtgtattgagactcacttttgatttcttcatctgt-ctattctgcttcccttctcattgtgaattgtac-ctatcctaacat-gttctattcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG
                                                             |||  | |||  ||    ||| |||   | |  | |||| | || | | ||    | ||||  | |  ||  |   | ||  ||| || | |  ||| |  ||||||||||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| ||||| || ||||||||||| |||
-------------------------------------------------------------gcaactatgtgctgg---tcatttt---tcttattatctatactgtaccgccatgcgtctcgctatatatgctgtacgattataagatagattcattgaaatgcagATTGTTGCCTTTCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATACAGCAAATTCATTGTTCAG

upper sequence: LOC_Os04g59494.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 13
gtatttttatcaattaactattgctgtatttaattccttgaacttcattaggaaaagagtagcatgtgtgtattgagactcacttttgatttcttcatctgtctattctgcttcccttctcattgtgaattgtacctatcctaacatgttctattc--atttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG
                                                                  |   | |||         ||    |   |  |   |||| | |  |    |     |  | |  |     |||  | |||   || ||||  |  |||||||||| |||||||| || || ||| | ||||||||||||||| | ||||| ||||||||||| |||||||| || || | ||| ||||||||||| |||
-----------------------------------------------------------------attcatcttgttctagttcttcaggtatctggttgctctaatattttcaagtaactgtattaatgtcaggttattgtgaca-actcaattcttacatgcagATTGTGGCTTTTCTCATCCCCCTTTTAGACGATAAATTTCCTTTGATACGAAGTATTACTTGCTGGACCCTTTCTCGGTTTAGCAAATTCATTGTTCAG

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|33797567|gb|CF324643.1|CF324643
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|29624708|gb|CB629719.1|CB629719
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATAC
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATAC
EST: gi|33678128|gb|CF306367.1|CF306367
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58668781|gb|CK057467.1|CK057467
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|29626307|gb|CB631318.1|CB631318
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58662574|gb|CK051260.1|CK051260
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCC
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCC
EST: gi|58612862|gb|CK040574.1|CK040574
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58672477|gb|CK061163.1|CK061163
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58666235|gb|CK054921.1|CK054921
EST:     ATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: ATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58656826|gb|CK045506.1|CK045506
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58663523|gb|CK052209.1|CK052209
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58608786|gb|CK036819.1|CK036819
EST:     GCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATAGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG

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: 66 (upstream exon), 70 (downstream exon)
Score: 38

AACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcccttctcattgtgaattgtacctatcctaacatgttctattcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG
                             tcctaac  putative branch site (score: 38)
                                       ttctattc  putative PPT
                                          tattcattt  TA-rich tract