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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtaatattgttttcaatctatcgtacacttcagcatgtatgtcaataagttcattatcatcccaagttacaataagtatttttatgttatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.5 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 17
--agtgtaatattgtt--ttcaatctatcgtacacttca--gcatgtatgtcaataagttcat-tatcatcccaagttacaat-aagt-atttttat-gttatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAG---GGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTG
  | ||| |  |  ||  |  |   ||  | ||| ||||  ||   ||  | ||    ||  | |||  | |  |||| || | |||| | | |||| ||| |||| ||||| ||||||||  | |||  |||| |||| |||    |||| || | | ||||| | |||||||||||||||||||| ||||||||||| ||||| ||||   
gtaatgtcacttcattaatataccttaatggacaattcatggctattagtttaactccttggtctatttttcttagttgcacttaagtcactattattgttgtttgatagGTGTTTCTTCCACACGATATTGATAAGAAGAAAAAGAGGAGGAAGAGCAGGAGTAATCCCATATTTTTTGCTGAACCAATGCGAGCATCAAATTCTTTTG---

upper sequence: LOC_Os12g01140.5 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 18
agtgtaatattgttttcaatctatcgtacacttcagcatgtatgtcaataagttcattatcatcccaagttacaataagtatttttatgttatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTG
   |||  |    | || || || |  | | |  |   | |   |||   | || | |   ||| ||      |||| |||| ||  || |  |||  || | ||  | ||  |      |||  ||||||        |||          |||| |||||  | |||||||||||||||||||| |||||||| ||||
---gtatcacaactatctat-tacccaagatt--aatttttggttcagagaattgaattatatcacataagcaaataggtatatt-gtgctcgttg-cagCTTTTGATGCCAAATACAAATGAAAAGAAAAGGCAACATAAAGGTCAACAGAACCCAATATTCATGGCTGAACCTATGCGAGCATCAAATTCATTCGTTG
















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|66913937|gb|CX100785.1|CX100785
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|86908120|gb|CI300633.1|CI300633
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29630467|gb|CB635476.1|CB635476
EST:     CTTGCAGACCGCAG                         TTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: CTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|88299110|gb|CI570080.1|CI570080
EST:     GTCTTGTCTAACATCTTGCAGACCGGAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: GTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|27334351|gb|CA882802.1|CA882802
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29630120|gb|CB635129.1|CB635129
EST:     TCTCCCTTACAGATTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29623926|gb|CB628937.1|CB628937
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29622724|gb|CB627735.1|CB627735
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29677072|gb|CB673347.1|CB673347
EST:     TTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataagttcattatcatcccaagttacaataagtatttttatgttatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTG
                     aagttacaataagtat  TA-rich tract