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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagaaattaccaacagatccctgttttgtcacctgaaggattcaaaaactccttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT

Basic information

species Oryza sativa
transcript LOC_Os02g52140.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 2
gtgcagaaattaccaacagatccctgttttgtcacctgaaggattcaaaaactccttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT
|| |||||||      ||||  |    |   |   |   ||  || ||| |   ||   ||   | ||||      ||  | |||    ||| || | ||||||| |||||| || || |||||||||||||||||||||||||||||||||||||| || || || ||||| || ||||| ||||| |||||||| ||||| || || |
gttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaaca-gcgcttttacttctgc--tctacc---tttttgctctgtgctccacagGTTGCGCCGAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G862331_T04 (Zea mays), 3'ss of exon 4
gtgcagaaattaccaacagatccctgttttgtcacctgaaggattcaaaaactccttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT
||||||||||  |  |     |   || |    |  |      ||  ||||| | | |  | |    |||      ||  |||||    ||  || | ||||||| |||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| || ||||| ||||| |||||||| || ||||| || |
gtgcagaaat-gcttatgttgcatggtctcaagagttcct--tttttaaaacacttgtcaatagtgctttacttctgc--tttacc---ttcttgctctgtgctctacagGTCGCCCCAAAGAGGACTAATGTTCCTGGGATGAAGCAGCGTCCACCACGTGGGTATAATCCATACCATGGCTACCCTTATAGATCATACGGGGCACCGT

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143163_T01 (Zea mays), 3'ss of exon 1
gtgcagaaattaccaacagatccctgttttgtcacctgaaggattcaaaaactccttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT
|| |||||||      ||||  |    |   |   |   ||  || ||| |   ||   ||    |||||      ||  |||||    ||| || | ||||||| |||||| || ||||||||||||||||||||||||||||||||||||||||| || || || ||||| || ||||| ||||| |||||||| ||||| || || |
gttcagaaatatttggcagaggctcaatgcttttgcaagagattttaaagaaatctcaacagcgctttttacttctgc--tttacc---tttttgctctgtgctccacagGTTGCGCCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCACGCGGGTATAATCCCTACCATGGCTACCCTTATAGATCATATGGAGCACCGT

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|86854695|gb|CI258986.1|CI258986
EST:     GGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCNCTGGGATGAAGCAGCGTCCACCGCGT
genomic: GGAGGCTCTGAATTTGAATGAATCTGAACTGCAT-GGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|86258520|gb|CI064873.1|CI064873
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|32948090|gb|BP184662.1|BP184662
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|87024798|gb|CI261307.1|CI261307
EST:     AGGAGGCCCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|87025376|gb|CI267742.1|CI267742
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|86491058|gb|CI133691.1|CI133691
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|87018233|gb|CI265525.1|CI265525
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|88847474|gb|CI015967.1|CI015967
EST:     AATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|66926559|gb|CX113407.1|CX113407
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|86505168|gb|CI147801.1|CI147801
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|86417997|gb|CI032206.1|CI032206
EST:     CTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: CTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|33664619|gb|CF295586.1|CF295586
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|88519815|gb|CI447469.1|CI447469
EST:     GCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTTCCCTGGGATGAAGCAGCGTCCACCGCG
genomic: GCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATG-TCCCTGGGATGAAGCAGCGTCCACCGCG
EST: gi|58598948|gb|CK009476.1|CK009476
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGTTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|32948232|gb|BP184804.1|BP184804
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|86255584|gb|CI065261.1|CI065261
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|33664620|gb|CF295587.1|CF295587
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|88222758|gb|CI220823.1|CI220823
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|88469773|gb|CI407044.1|CI407044
EST:     GGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: GGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|87032407|gb|CI264188.1|CI264188
EST:     GTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: GTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
EST: gi|88980934|gb|CI021061.1|CI021061
EST:     AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAG                         GTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT
genomic: AGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGT

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: 69 (upstream exon), 66 (downstream exon)
Score: 7

ACAGCCAAAAGGTTTTGCTTATGTGGAATTTCTGGAACAAGAAGCAGTTCAGGAGGCTCTGAATTTGAATGAATCTGAACTGCATGGTCGTCAGATAAAGgtgcagaaat ... tgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcacatgtttttgtcctcgcaatttactcaatttctgttttgtgctcaacagGTGGCACCAAAGAGGACTAATGTCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCAT
                       aatttactcaattt  TA-rich tract