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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACGTTTACCCCAACGTCAACAGCGTCGGCGCGGGCCTCTTCCTCAACGAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccctccatttgcacaacgatttgcttgctagtttttcaattgcgttgcgtgcgagtatgcaactgtgccag

Basic information

species Zea mays
transcript GRMZM2G328908_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G328908_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 2
GCTACGTTTACCCCAACGTCAACAGCGTCGGCGCGGGCCTCTTCCTCAACGAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgaga-----gccctccatttgcacaacgatttgcttgc--tagtttttcaattgcgttg-------cgtgcgagtatgcaactgtgccag--------
|||| |||||||||||||||||||||| |||||| || || ||||||| ||||||||||  | ||||||| | ||||||||||||| |||| ||| |||||| |||       |||||  ||   |   | || || | |  | | ||   || ||   |        | | |||  | |  ||||     |        
GCTATGTTTACCCCAACGTCAACAGCGCCGGCGCCGGGCTGTTCCTCACCGAGATGTTCCGGCCGCCGACCACCAACCTCGCCGACAGCGGCTACAACATgtaagatcatcatcctcctcttctccgcggtttcgcctccccttggttcataactgttataatttcctcatccgaaaaagttactgctttggcattcttg
















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|7135782|gb|AW498263.1|AW498263
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|148991813|gb|EE033399.2|EE033399
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|12046207|gb|BF728346.1|BF728346
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|148947609|gb|EC893089.2|EC893089
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|148928663|gb|EC873223.2|EC873223
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|7304624|gb|AW600563.1|AW600563
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATG
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATG
EST: gi|13198763|gb|BG354565.1|BG354565
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|13490371|gb|BG517135.1|BG517135
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|149081398|gb|EE170514.2|EE170514
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|149097400|gb|EE183253.2|EE183253
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|148996081|gb|EE035340.2|EE035340
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|116815101|gb|EC857735.1|EC857735
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGACGGCGAAGAACGTACCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|6827348|gb|AW330991.1|AW330991
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|148934031|gb|EC878039.2|EC878039
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
EST: gi|149040129|gb|EE046780.2|EE046780
EST:     GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACAT                         GTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA
genomic: GAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GCTACGTTTACCCCAACGTCAACAGCGTCGGCGCGGGCCTCTTCCTCAACGAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCAGCAGCCGACACAGCCGCTGCGGGTGTCCATCTCCAAGAAGCTACGGGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

GCTACGTTTACCCCAACGTCAACAGCGTCGGCGCGGGCCTCTTCCTCAACGAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccc ... actgtgccagGTATAAAGACATGCTGGAGTGGATCGGCCGGCCGGCGAAGAACGTTCCCCAGCAGCCGACACAGCCGCTGCGGGTGTCCATCTCCAAGAAGCTACGGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACGTTTACCCCAACGTCAACAGCGTCGGCGCGGGCCTCTTCCTCAACGAGATGTTCAAGGCGCCGACTAACAACCTCGCCGACGGCGGGTACCACATgtgagagccctccatttgcacaacgatttgcttgctagtttttcaattgcgttgcgtgcgagtatgcaactgtgccag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGCGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGCCGACG