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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_Os04g59494.1
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|58612862|gb|CK040574.1|CK040574
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|33797567|gb|CF324643.1|CF324643
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|33678128|gb|CF306367.1|CF306367
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGG
EST: gi|58662574|gb|CK051260.1|CK051260
EST:     GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAG                         ATTGTTGCTTTTCTTATTCC
genomic: GTGCTATAGCGGAGGGATGCATTACTGGGCTATATCCCCATCTTCCGCAGgtatttttat ... tcatttgcagATTGTTGCTTTTCTTATTCC
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcccttctcattgtgaattgtacctatcctaacatgttctattcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG
                             tcctaac  putative branch site (score: 1)
                                       ttctattc  putative PPT
                                          tattcattt  TA-rich tract