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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctctgtttcccactcccacgctccggttggtgcttgcttttggcttgaaatcgctagatcggatctgctgaggtgcttgggtgggttgcggact...

Basic information

species Zea mays
transcript GRMZM2G359018_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G359018_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 5'ss of exon 1
TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctctgtttcccactcccacgctccggttggtgcttgcttttggcttgaaatcg--ctagatcggatctgctgaggtgcttgggtgggttgcggact---
|| || | || | || || ||||||||||||||||||||||||||||||||||| |||||| ||||||||||||||| || ||||||||||| ||||||||| | | | | | || | | | || | || | | | | | || || | | | |||| | |||
GTTGATTCGGCTGCTGCTGCCGCGGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGGCGCGAGGAGCCCATCCACAAGGTCCTCGGTGGAGGCAAACgtatggctgctctctctctgctgatgatctctct-----ctctctctgtttcaaagctgatttggtttgaatttgttagagcgggtggggatgggctggatctgg
















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|211159044|gb|FL114486.1|FL114486
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCCCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211157454|gb|FL114477.1|FL114477
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159038|gb|FL114480.1|FL114480
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211157447|gb|FL114470.1|FL114470
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159041|gb|FL114483.1|FL114483
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159046|gb|FL114488.1|FL114488
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|14883562|gb|BI273418.1|BI273418
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|29543943|gb|CB604323.1|CB604323
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159040|gb|FL114482.1|FL114482
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|15554133|gb|BI644131.1|BI644131
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211157452|gb|FL114475.1|FL114475
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTG-TGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAG
EST: gi|211157455|gb|FL114478.1|FL114478
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159043|gb|FL114485.1|FL114485
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGA
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGA
EST: gi|211157450|gb|FL114473.1|FL114473
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159045|gb|FL114487.1|FL114487
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211157448|gb|FL114471.1|FL114471
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
EST: gi|211159039|gb|FL114481.1|FL114481
EST:     CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGC                         CTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG
genomic: CCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTG

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: 48 (upstream exon), 48 (downstream exon)
Score: 125

TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 37

TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 49

TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 48

TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctct ... tattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGACTCCACCGCCACGGCGGCCGCCGAGGCCAAGGCCAAGGTGTTCCGCCTCTTCGGCCGCGAGCAGCCCATCCACAAGGCGCTTGGTGGAGGCAAGCgtatggctctgtttcccactcccacgctccggttggtgcttgcttttggcttgaaatcgctagatcggatctgctgaggtgcttgggtgggttgcggact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG