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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcggtttctccttccttactcttctcctacattagctgcaactagcacatctttttttttagagttgattttgatttttggtactagttcaaat...

Basic information

species Zea mays
transcript GRMZM2G177445_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177445_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 5'ss of exon 3
AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgt--tcggttt---ctccttccttactcttctcctacattagctgcaactagcacatcttttttt--ttagagttgattttgatttttggtactagttcaaat
 |||||||||| |||||||| |||||||||||||  |||||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||  | |||     |   ||  ||  |||| | ||| | |||||||| ||| || ||     |||    |  |||| ||  |||||       |||| |||| 
CGGCTGGCCAACCTGATCGGCTGCTGCTGCGAGAATGGCGAGCGGCTGCTCGTCGCGGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgtgtttggtgctcaccttttttttcttcttgttctatactagctgcagcta-catattgggctttggcaaatgttgtttccgattt-----ggtagtacaaa-
















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|101385419|gb|EB814755.1|EB814755
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
EST: gi|211337353|gb|FK979584.1|FK979584
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAA-TCCATTGAGTTGG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGG
EST: gi|149023559|gb|EE045892.2|EE045892
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
EST: gi|148967635|gb|EE018892.2|EE018892
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
EST: gi|148996262|gb|EE035542.2|EE035542
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
EST: gi|76281723|gb|DV021291.1|DV021291
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGGCA-TGAGGATGAGGGCTGCGCTTTAT
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGG-CAATGAGGATGAGGGCTGCGCTTTAT
EST: gi|211337354|gb|FK979585.1|FK979585
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAAT
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAAT
EST: gi|93284518|gb|EB676782.1|EB676782
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGANCAA-TCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTAT
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGA-CAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTAT
EST: gi|71440119|gb|DR821169.1|DR821169
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
EST: gi|71447053|gb|DR828103.1|DR828103
EST:     GTCGCAGAGTTCATGCCGCACGAGACCTTTGG-AAAGCATCTCTTCCACT                         GGGAAACAAATCCCTTGAGTTG
genomic: GTCGCAGAGTTCATGCCGCACGAGACCTT-GGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTG
EST: gi|148931103|gb|EC873754.2|EC873754
EST:     CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACT                         GGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG
genomic: CGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATG

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), 48 (downstream exon)
Score: 51

AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATGTGGCACAAGCGTTGGACTACTGCAGTAGCAAAGGGAGGGCACTCTATCA


Block sizes: 46 (upstream exon), 37 (downstream exon)
Score: 9

AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATGTGGCACAAGCGTTGGACTACTGCAGTAGCAAAGGGAGGGCACTCTATCA


Block sizes: 17 (upstream exon), 37 (downstream exon)
Score: 3

AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATGTGGCACAAGCGTTGGACTACTGCAGTAGCAAAGGGAGGGCACTCTATCA


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 10

AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcgg ... tatgtggtagGGGAGACAAATCCATTGAGTTGGGCAATGAGGATGAGGGCTGCGCTTTATGTGGCACAAGCGTTGGACTACTGCAGTAGCAAAGGGAGGGCACTCTATCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTGGCCAATCTGATCGGTTGCTGCTGCGAGAGCGGCGAGCGTCTCCTCGTCGCAGAGTTCATGCCGCACGAGACCTTGGCAAAGCATCTCTTCCACTgtatgttcggtttctccttccttactcttctcctacattagctgcaactagcacatctttttttttagagttgattttgatttttggtactagttcaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttcc