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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATCAAGCTTTACCGAGCATGTCCCTTATTGCTTCAGACTTCAGCTATCTTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcctggcagactgcgattttattaagcatgcaaagctttattttttttaactactacatttctccaactaggctgcgaaggctacttattatt...

Basic information

species Zea mays
transcript GRMZM2G101217_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T07 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 5'ss of exon 10
ACATCAAGCTTTACCGAGCATGTCCCTTATTGCTTCAGACTTCAGCTATCTTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtg--agtgtcctggcagactgcgattttattaagcatgcaaagctttattttttttaactactacatt---tctccaactaggctgcgaaggctacttattatt
|||||||||||| || |||||||||||||| |||||||| |||||||||||||| || || || |||||||| || || |||||||||||||| |||||||||  |    | |  | ||||     |   ||   |   ||| ||   |||| | |     ||  | ||     |    |  |  |||                 
ACATCAAGCTTTGCCAAGCATGTCCCTTATAGCTTCAGATTTCAGCTATCTTCCTGATGTCAGTATACCTGGCGATAGAGCTCCATTGGTTTCTTCAAAGgtgacaagaccttcactgacttttggtgcgtttttccaacaaggca--atttctctaggacacctcgttgatgttgtgtcctgcttgcag---------------
















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|50337134|gb|CO532260.1|CO532260
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|93012640|gb|EB638160.1|EB638160
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         GATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG
EST: gi|71418851|gb|DR804567.1|DR804567
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|50336105|gb|CO531231.1|CO531231
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         A
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaag-
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         A
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaag-
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAG                         A
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaag-
EST: gi|50325601|gb|CO520727.1|CO520727
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|76281531|gb|DV021099.1|DV021099
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|148960596|gb|EE011218.2|EE011218
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|60352980|gb|DN219953.1|DN219953
EST:     ACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: ACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga
EST: gi|76924071|gb|DV169789.1|DV169789
EST:     TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGAAG                       
genomic: TTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATC--A-AAGgtgagtgtcc ... attgtaga

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 2

ACATCAAGCTTTACCGAGCATGTCCCTTATTGCTTCAGACTTCAGCTATCTTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 3

ACATCAAGCTTTACCGAGCATGTCCCTTATTGCTTCAGACTTCAGCTATCTTCCAGACGTTAGCATACCTGGTGACAGGGCTCCATTGGTTTCATCAAAGgtgagtgtcc ... attgtagaagGATGGGAAGACATCAGATCATCGCAACTACTTTGATGCTCAG




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