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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctggaattgcag

Basic information

species Zea mays
transcript GRMZM2G026470_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 4
GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcccgagacgga-----ccaataatccccactcccc-------------atatctagagtcttttacttaccaagcaaagcgctggaattgcag---------------------------
||||| || ||||| ||  | |||||||| ||||||||||| || |||||||||||||| || |||||| |     | |  |        |   |||  |  |||                 ||| ||   ||| ||||  || |  ||||   |||   | ||||                            
GAACCAGTTCTTCCTGGTTCATTCCTCCGAGCCAGGGCCATTGGTCTCATGCCTATGATTGACCAGgtaagtaaatcaatccattcatctctgctaagtcaaactttattagggagaaaaaaataacttttgtcatttaagtatcg-gcaacaagcttacactgcacctgcatttttttccgtttcatgaacag
















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|20300588|gb|BQ163531.1|BQ163531
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|71331881|gb|DR802819.1|DR802819
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|28984521|gb|BQ539133.2|BQ539133
EST:     ATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: ATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|60352307|gb|DN219280.1|DN219280
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGA
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGA
EST: gi|71331880|gb|DR802818.1|DR802818
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|20300295|gb|BQ163238.1|BQ163238
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|211434006|gb|FL392555.1|FL392555
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|60400572|gb|DN233379.1|DN233379
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|78121801|gb|DV540185.1|DV540185
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTTTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|5499294|gb|AI855161.1|AI855161
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGCCCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|60354156|gb|DN221129.1|DN221129
EST:     ATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: ATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|60344571|gb|DN211544.1|DN211544
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC
EST: gi|20300766|gb|BQ163709.1|BQ163709
EST:     GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAG                         GGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCCAGTAC
genomic: GCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTAC

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: 45 (upstream exon), 49 (downstream exon)
Score: 19

GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 437

GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcc ... ggaattgcagGGAGAGAAGGACGACAAGATCATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCCGTCCTTCCCGGCGCCTTCCTCCGCGCCAGGGCCATCGGCCTCATGCCTATGATAGATCAGgtaggccgcccgagacggaccaataatccccactccccatatctagagtcttttacttaccaagcaaagcgctggaattgcag

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