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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGCCCCTTCAACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcgtattgctcctcctgcgctccccgattcgtcgacgaaatttccaggggaaaaaatcaggatctggaaagacttcagatgtgttttttttgtatgttttccctttggaagttcggtaaaacattgcttctgtttgtgtgttggctggcctccgcag

Basic information

species Zea mays
transcript GRMZM2G018950_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018950_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g29620.1 (Oryza sativa), 5'ss of exon 2
GCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGCCCCTTCAACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcgtattgctcctcctgcgctccccgattcgtcgacgaaatttccaggggaaaaaatcaggatctggaaagacttcagatgtgttttttttgtatgttttccctttggaagttcggtaaaa-cattgcttctgtttgtgtgttggctggcctccgcag
 ||||||||||||||||||||||||||||||||||||||||| || ||| |||| || |||||| |||| ||||||||||| || ||||| |||||  ||||||||                                    | ||  |||   |  ||  |||||  | || |    | ||  | | | || ||    ||||   |   ||| |  | | | | | | |||||  |    || |    | || |          
CCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGGCCGTTCCACATCGCCGACAACATGTCTCTCGTCTGGAACGACTTTGGCTGGGATCAGgtacac------------------------------------caaaccttct--gataatcaatcataagctagtggtaattttgctatattgttacaatatgccatttgttttgttgattgttgagatcattgtgtaaaatttttcaattgcag----------
















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|211492802|gb|FL021489.1|FL021489
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCC
EST: gi|8368890|gb|BE051835.1|BE051835
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGCTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTG
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTG
EST: gi|211492815|gb|FL021502.1|FL021502
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGA
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGA
EST: gi|211272024|gb|FL427188.1|FL427188
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211495691|gb|FL021505.1|FL021505
EST:     CATAGNGGACAACTTGTCGCTCGTCTGGAATGATTTTTGGTTGGGACAAG                         GNATCAAATCTTATCTATGTCGAACAAGCCCACTGGAACTGGGTTTAGTTA
genomic: CATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTT-GGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCA-GCCCACTGGAACTGGGTTTAGTTA
EST: gi|148944673|gb|EC889809.2|EC889809
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211492812|gb|FL021499.1|FL021499
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGNTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGG
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGG
EST: gi|148944669|gb|EC889804.2|EC889804
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211495692|gb|FL021506.1|FL021506
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGAC
EST: gi|149099579|gb|EE185618.2|EE185618
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|148969832|gb|EE020724.2|EE020724
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211489928|gb|FL021487.1|FL021487
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTT
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTT
EST: gi|31360633|gb|CD444990.1|CD444990
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGCTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211492804|gb|FL021491.1|FL021491
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGNCGACCAGCCCCACTGGNAACTGGGGTTTAGT
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCC-ACTGG-AACTGGG-TTTAGT
EST: gi|211495694|gb|FL021508.1|FL021508
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAAGCCCACTGGGAACTGGGTTTTAGT
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCA-GCCCACTGG-AACTGGGTTT-AGT
EST: gi|211492810|gb|FL021497.1|FL021497
EST:     TAGCGGACAACTTGTCGCTTCGTCTGGAATGGATTTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGC
genomic: TAGCGGACAACTTGTCGCT-CGTCTGGAATG-ATTTT-GGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGC
EST: gi|211492803|gb|FL021490.1|FL021490
EST:     CATAGCGGACAACTTGTCGCTCGTCTGGAATGGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAAC
genomic: CATAGCGGACAACTTGTCGCTCGTCTGGAATG-ATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAAC
EST: gi|148941808|gb|EC886775.2|EC886775
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|148962748|gb|EE013659.2|EE013659
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211495693|gb|FL021507.1|FL021507
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGT
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGT
EST: gi|211492811|gb|FL021498.1|FL021498
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAAATGGGT
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGT
EST: gi|211492814|gb|FL021501.1|FL021501
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGGAACTGG
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGG-AACTGG
EST: gi|149005158|gb|EE039693.2|EE039693
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|15554170|gb|BI644168.1|BI644168
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAA
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAA
EST: gi|211492806|gb|FL021493.1|FL021493
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|149078258|gb|EE167015.2|EE167015
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|149110190|gb|EE294008.2|EE294008
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
EST: gi|211492807|gb|FL021494.1|FL021494
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAG
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAG
EST: gi|211334945|gb|FL422005.1|FL422005
EST:     -CATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACA-G                         GCATCAAATCTTATCTATGTC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTC
EST: gi|213187795|gb|FM187023.1|FM187023
EST:     ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGCTGGGACAAG                         GCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC
genomic: ACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTAC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

GCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGCCCCTTCAACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTACAGCTCGGATTCGCGTGACACTCGCCACAACGAAGCTACTATTAGCAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

GCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGCCCCTTCAACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTACAGCTCGGATTCGCGTGACACTCGCCACAACGAAGCTACTATTAGCAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

GCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGCCCCTTCAACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTACAGCTCGGATTCGCGTGACACTCGCCACAACGAAGCTACTATTAGCAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 307

GCCCGGCTGCAGCAGCGAGCTCGCGCTCTTCTACGAGAACGGCCCCTTCAACATAGCGGACAACTTGTCGCTCGTCTGGAATGATTTTGGTTGGGACAAGgtacacgtcg ... gcctccgcagGCATCAAATCTTATCTATGTCGACCAGCCCACTGGAACTGGGTTTAGTTACAGCTCGGATTCGCGTGACACTCGCCACAACGAAGCTACTATTAGCAATG