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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccccttctccatcatcacactctcggccctcaaccaacccccatttgccatcctgttgcatgcagtagctgaacctgactcttttctcttcggttacgcag

Basic information

species Zea mays
transcript GRMZM2G153977_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153977_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 11
TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccccttctccatcatcacactctcggccctcaaccaacccccatttgccatcctgttgcatgcagtagctgaacctgactcttttctcttc--ggttacgcag-------------------------------------------------------
||| |||||||||||| | |||||||||| ||| ||||  |||||||| || ||| | ||||||||||||||||| |||||    ||||| || ||  |||| | ||    ||||  ||  |  | ||        |    |  |||     ||| |||  | |      |  || || ||  |  |     | | ||  | ||  | ||                                                       
TCCAATGGGAGAATCATCTGTGGACTGTGGCAGCCTTGCATCCATGCCTGAGATTTCATTCACCATTGGAGGCAAAAAGTTTGCACTGAAGCCAGAAGAGgt-gcgatgatttctttatggtttctcttctttttttt---cttcccttgggtgc-atctagattagctgaaaagttggacacgcttgccggcccatctagtttgtgtagatatttgacgcactggcttgagcacataatttactctcttcttttggttgtgcag
















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|108823997|gb|EC278005.1|EC278005
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|211422086|gb|FL442273.1|FL442273
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|60344077|gb|DN211050.1|DN211050
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|67016864|gb|CO445613.1|CO445613
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|60400185|gb|DN232992.1|DN232992
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|60339829|gb|DN206802.1|DN206802
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|21331514|gb|BQ486895.1|BQ486895
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCA
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCA
EST: gi|211224716|gb|FL222434.1|FL222434
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|47962710|gb|CN845419.1|CN845419
EST:     GAAGTTCAAGCTGAAACAGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: GAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|60352456|gb|DN219429.1|DN219429
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|211287001|gb|FL447773.1|FL447773
EST:     AGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: AGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|211420574|gb|FL478622.1|FL478622
EST:     GCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: GCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|78120564|gb|DV538948.1|DV538948
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|16927203|gb|BM080272.1|BM080272
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|31405529|gb|CD484261.1|CD484261
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|32803015|gb|CD955251.1|CD955251
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|67015196|gb|CO443945.1|CO443945
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|32867897|gb|CF007579.1|CF007579
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|60354188|gb|DN221161.1|DN221161
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|60396263|gb|DN229132.1|DN229132
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTC
EST: gi|110519064|gb|EE023651.1|EE023651
EST:     GGCAAGAAGTTCAAGCTGAAACCGGAGCAG                         TACATTTTGAAGGTCGGTGGAAGGACAAGGTGCCCCAGTGCATCAGTGGAT
genomic: GGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGT-GAAGGACAAGCTG-CCCAGTGCATCAGTGGAT

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: 372

TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 814

TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 874

TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 732

TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccc ... ggttacgcagTACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCATGGGAGAATCAGCCGTGGACTGTGCCAGTCTTGGGTCCATGCCCGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCGGAGCAGgtcgtgaccccttctccatcatcacactctcggccctcaaccaacccccatttgccatcctgttgcatgcagtagctgaacctgactcttttctcttcggttacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG