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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctgctgtcgtcaaacgcccccgtctcgtgcgtcgactgctcgccgtgtacggtttcaccttcacctgcctatttgtttagattcgatagtcag...

Basic information

species Zea mays
transcript GRMZM5G868664_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868664_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g33790.1 (Oryza sativa), 5'ss of exon 1
AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctgctgtcgtcaaacgcccccgtctcgtgcgtcgactgctcgccgtgtacggtttcaccttcacctgcctatttgtttagattcga--tagtcag
||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||  ||||| |||||||||  |      | |  |  |||| |     | | | ||  |   | ||  | ||   | | | | ||  | |||   ||  ||  ||| || 
AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTCCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACCAACACCGTCCCCTGgtcagtgctgctccccatccccccttcgatctcttctcctgcccgttccgctcttgcg-ctgcagaatgatccggctgat-gttgcaataggatttaggcac
















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|148986836|gb|EE030636.2|EE030636
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|32802619|gb|CD954855.1|CD954855
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|211517263|gb|FK995258.1|FK995258
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|211517262|gb|FK995257.1|FK995257
EST:     AAGSGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAAKGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|32805037|gb|CD957273.1|CD957273
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|211517264|gb|FK995259.1|FK995259
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|211517265|gb|FK995260.1|FK995260
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|211449265|gb|FL470101.1|FL470101
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|21389934|gb|BQ527983.1|BQ527983
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|32788095|gb|CD940331.1|CD940331
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACCG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|32795035|gb|CD947271.1|CD947271
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGTTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|71332520|gb|DR803224.1|DR803224
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
EST: gi|211449266|gb|FL470102.1|FL470102
EST:     AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTG                         GTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG
genomic: AAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG

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: 39 (upstream exon), 38 (downstream exon)
Score: 19

AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG


Block sizes: 39 (upstream exon), 38 (downstream exon)
Score: 72

AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 52

AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG


Block sizes: 45 (upstream exon), 38 (downstream exon)
Score: 55

AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctg ... gatcatgcagGTACCATGCCAACAGAATGCTTAGCTTTTACGCACCAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCACCGGGATGACGCGCCCGCTCGTCGAGATCCTGCGGGACCTCAACAAGCGCGTCCCCGACAAGATCATCGACCCCGACACTAACACCGTCAACTGgtgagtgctgctgtcgtcaaacgcccccgtctcgtgcgtcgactgctcgccgtgtacggtttcaccttcacctgcctatttgtttagattcgatagtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccccc