Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaactagacttagttatttctatttgcctatttgtgcataaaataatggcatgcactgcctaatttattattattcataaaaacttaagttgata...

Basic information

species Zea mays
transcript GRMZM5G824831_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824831_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 5
GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact--agacttagttatttctatttgcc-tatttgtgcataaaataatggcatgcactgcctaatttattattattcataaaaacttaagttgata
|||  ||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||| |||||||  |||  ||| ||    ||||||||      ||||  |  |||| ||| |      |     | |  | |||| | |  ||  | |  |  || |   
GAAACTATCCCTGTTACTCAGCTTGTCCGAGAAACTGCTGCTGTTATGCAGGAGTTCACACAGTCTGGgtatgctacttcagagttttccatttctatcaatgatattgttaaataatatattcttgcacttgttcgacctaattaatttgtatggatatatttgtgg---

upper sequence: GRMZM5G824831_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S61_202V6.1 (Physcomitrella patens), 5'ss of exon 6
GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaactagacttagttatttctatttgcctatttgtgcataaaataatggcatgcactgcctaatttattattattcataaaaacttaagttgata
||||  || ||  |  | ||  | ||  ||||||| ||||| || ||||||||||||||||| |||||||  | |  |   | | |||||||    |   |  | |     ||  |   ||  ||            || | | | ||     | | | |  || |||
GAACCCATTCCATTGTCGCAATTGGTTAGAGAGACAGCTGCAGTGATGCAGGAGTTCACACAATCAGGgtgcgaatttcttcgtggttattttagatgctccttgtcaagctatgactttgagatttctattggtgcttctaagtgttttgggatattgagattaata
















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|71445140|gb|DR826190.1|DR826190
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACCA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211156514|gb|FL164228.1|FL164228
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAKTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGT
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGT
EST: gi|74241051|gb|DT648965.1|DT648965
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         G
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcag-
EST: gi|74241051|gb|DT648965.1|DT648965
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         G
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcag-
EST: gi|211269953|gb|FL444406.1|FL444406
EST:     CAGTTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|6952542|gb|AW424610.1|AW424610
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|148956338|gb|EC902144.2|EC902144
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211264909|gb|FL208725.1|FL208725
EST:     AGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAAGT-CACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: AGCTTGTACGAGAGACTGCTGCTGTCATGCAGGA-GTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|78112696|gb|DV531090.1|DV531090
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|148952476|gb|EC898302.2|EC898302
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGAGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211264914|gb|FL208730.1|FL208730
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGAC
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGAC
EST: gi|149076954|gb|EE165611.2|EE165611
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|78112697|gb|DV531091.1|DV531091
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211252214|gb|FK953395.1|FK953395
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTT
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTT
EST: gi|5268558|gb|AI770522.1|AI770522
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGTAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211149323|gb|FL312581.1|FL312581
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32830197|gb|CD969875.1|CD969875
EST:     ACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: ACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|148987620|gb|EE031494.2|EE031494
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211154922|gb|FL164220.1|FL164220
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGA
EST: gi|211252215|gb|FK953396.1|FK953396
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|6194486|gb|AW146590.1|AW146590
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|71447361|gb|DR828411.1|DR828411
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211158115|gb|FL164244.1|FL164244
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTG
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTG
EST: gi|67024880|gb|CO453629.1|CO453629
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32795340|gb|CD947576.1|CD947576
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211321302|gb|FL273340.1|FL273340
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211153313|gb|FL164201.1|FL164201
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTG
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTG
EST: gi|211153309|gb|FL164197.1|FL164197
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA

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), 47 (downstream exon)
Score: 541

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 359

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 300

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 316

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaactagacttagttatttctatttgcctatttgtgcataaaataatggcatgcactgcctaatttattattattcataaaaacttaagttgata

- - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - GCTGCT